MACRO TestDebug1 "TestDebug1 Macro" FOR EACH BioSource DO o = Resolve("org.orgname.mod") Where o.subtype = "isolate"; SetQual(o, "subname", "new isolate"); DONE ------------------------------------------------------------------------------ MACRO TestDebug2 "TestDebug2 Macro" FOR EACH BioSource Where EQUALS("subtype","country", "Denmark") DO o = Resolve("org"); SetQual(o, "taxname", "new taxname"); DONE ------------------------------------------------------------------------------ MACRO TestDebug3 "TestDebug3 Macro" VAR Qual_Name = %pcr-primers..forward..name% FOR EACH BioSource DO RemoveQual(Qual_Name); DONE ------------------------------------------------------------------------------ MACRO TestDebug4 "TestDebug4 Macro" VAR qual_name = "data.prot.desc" FOR EACH SeqFeat WHERE IS_SEQ_AA("location") DO SetStringQual(qual_name, "new protein description", "eReplace"); DONE ------------------------------------------------------------------------------ MACRO TestDebug5 "TestDebug5 Macro" For each Cdregion Where ISDISTFROMSTART("location", "> 3") Do RemoveQual("comment"); Done ------------------------------------------------------------------------------ MACRO TestDebug6 "TestDebug6 Macro" Var cs = true For each Gene Where ISUPPER(BIOSOURCE_FOR_SEQFEAT("org.taxname")) Do SetStringQual("data.gene.locus", "new gene locus", "eReplace"); Done ------------------------------------------------------------------------------ MACRO TestDebug7 "TestDebug7 Macro" Var cs = true For each Cdregion Where CONTAINS(GENE_FOR_CDS("data.gene.locus"), "Hypothetical", cs) Do ExtendFeatToSeqStart(); Done ------------------------------------------------------------------------------ MACRO TestDebug8 "TestDebug8 Macro" VAR qual_name = "data.prot.desc" FOR EACH Protein WHERE GENE_FOR_PROTEIN("data.gene.locus") = "Hypothetical protein gene" DO o = Resolve("data.prot.name"); SetStringQual(o, "", "new protein name", "ePrepend", ":"); DONE ------------------------------------------------------------------------------ MACRO TestDebug9 "TestDebug9 Macro" VAR qual_name = "data.prot.desc" FOR EACH Cdregion WHERE CONTAINS(GENE_FOR_CDS("comment"), "comment") DO ExtendFeatToSeqStop(); DONE ------------------------------------------------------------------------------ MACRO TestDebug10 "TestDebug10 macro" VAR find_text = "Sandro" repl_text = "Sandor" location = "anywhere" case_sensitive = true FOR EACH Pubdesc WHERE PUB_AFFIL("pub", "sub") = "Saxony" DO obj = PUB_AUTHORS("pub.", "first"); EditStringQual(obj, "", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO TestDebug11 "TestDebug11 Macro" FOR EACH BioSource DO o = Resolve("org.orgname.mod") Where o.subtype = "nat-host"; RemoveModifier(o); DONE ------------------------------------------------------------------------------ MACRO TestDebug12 "TestDebug12 Macro" FOR EACH Protein DO RemoveInvalidECNumbers(); DONE ------------------------------------------------------------------------------ MACRO TestDebug13 "TestDebug13 Macro" Var del_improper = true del_unrecog = true del_mult_repl = true For each Protein Do UpdateReplacedECNumbers(del_improper, del_unrecog, del_mult_repl); Done ------------------------------------------------------------------------------ MACRO TestDebug14 "TestDebug14 Macro" For each Cdregion Do ApplyCDSFrame("best"); Done ------------------------------------------------------------------------------ MACRO TestDebug15 "TestDebug15 Macro" For each Cdregion Do ApplyCDSFrame("match"); Done ------------------------------------------------------------------------------ MACRO TestDebug16 "TestDebug16 macro" FOR EACH Pubdesc DO obj = PUB_AFFIL("pub.", "sub"); RemoveQual(obj); DONE ------------------------------------------------------------------------------ MACRO Altitude_fix_macro "Fix altitude" For each BioSource Do obj = Resolve("subtype") where obj.subtype = "altitude"; FixFormat(obj); Done ------------------------------------------------------------------------------ MACRO Remove_five_qualifiers "Remove isolate, strain, note-subsource, culture-collection, specimen-voucher" FOR EACH BioSource DO obj = Resolve("org.orgname.mod") WHERE obj.subtype = "isolate" OR obj.subtype = "strain" OR obj.subtype = "culture-collection" OR obj.subtype = "specimen-voucher"; RemoveModifier(obj); subsrc = Resolve("subtype") WHERE subsrc.subtype = "other"; RemoveModifier(subsrc); DONE ------------------------------------------------------------------------------ MACRO ApplyGenBankTypeToWGSSets "Apply genbank set type to wgs sets" FOR EACH SeqSet WHERE class = "wgs-set" DO SetQual("class", "", "genbank"); DONE ------------------------------------------------------------------------------ MACRO Seq_Feat_MoveGeneLocusToNote "Use known abbreviation for note instead of locus" VAR OldLocusValue = %Putative terminase large subunit gene% NewLocusValue = %NEW LOCUS VALUE% Taxname = %Methanobacterium formicicum phage% FOR EACH SeqFeat WHERE CHOICETYPE("data") = "gene" AND data.gene.locus = OldLocusValue AND BIOSOURCE_FOR_SEQFEAT("org.taxname") = Taxname DO SetStringQual("data.gene.locus", NewLocusValue, "eReplace"); SetStringQual("comment", OldLocusValue, "eReplace"); DONE ------------------------------------------------------------------------------ MACRO Seq_Feat_SetProteinName "Set cytochrome oxidase protein name" VAR Locus = %COX1% ProteinName = %cytochrome oxidase 1% FOR EACH SeqFeat WHERE CHOICETYPE("data") = "cdregion" AND GENE_FOR_CDS("data.gene.locus") = Locus DO SetStringQual("comment", ProteinName, "eReplace"); DONE ------------------------------------------------------------------------------ MACRO BioSource_Apply_String_Value "Macro applies string value to biosource qualifier" Var Qualifier = %org.taxname% Value_To_Apply = %uncultured% Handle_existing_text = choice { "eReplace", "ePrepend", "eAppend", "eLeaveOld"} Delimiter = %;% For each BioSource Do SetStringQual(Qualifier, Value_To_Apply, Handle_existing_text, Delimiter); Done ------------------------------------------------------------------------------ MACRO BioSource_Remove_Qualifier "Macro removes a qualifier from a biosource" Var Qualifier = %org.taxname% For each BioSource Do RemoveQual(Qualifier); Done ------------------------------------------------------------------------------ MACRO BioSource_Copy_Qualifier "Macro copies org.taxname value to org.common" Var Qual_src = %org.taxname% Qual_dst = %org.common% Handle_existing_text = choice { "eReplace", "ePrepend", "eAppend", "eLeaveOld" } For each BioSource Do CopyStringQual(Qual_src, Qual_dst, Handle_existing_text); Done ------------------------------------------------------------------------------ MACRO BioSource_Convert_Taxname_To_Common "Macro converts org.taxname to org.common" Var Qual_src = %org.taxname% Qual_dst = %org.common% Handle_existing_text = choice { "eReplace", "ePrepend", "eAppend", "eLeaveOld" } Delimiter = %,% For each BioSource Do CopyStringQual(Qual_src, Qual_dst, Handle_existing_text, Delimiter); RemoveQual(Qual_src); Done ------------------------------------------------------------------------------ MACRO BioSource_Swap_Qualifiers_Example1 "Macro swaps two string qualifiers. Both are uniquely idetifiable by their field names." Var Qual_1_Name = %org.taxname% Qual_2_Name = %org.common% For each BioSource Do SwapQual(Qual_1_Name, Qual_2_Name); Done ------------------------------------------------------------------------------ MACRO BioSource_Edit_Qualifier "Replace a text in org.taxname" VAR qual_name = %org.orgname.mod.subname% find_text = %um% repl_text = %UM% location = choice {"at the beginning", "at the end", "anywhere" } case_sensitive = false FOR EACH BioSource DO EditStringQual (qual_name, find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Seq_Feat_Remove_Qualifier "Macro removes Seq-Feat qualifier" Var qual_name = %data.gene.locus% For each Gene Where ISUPPER(qual_name) Do RemoveQual(qual_name); Done ------------------------------------------------------------------------------ MACRO Apply_String_Value_wConstraint "Macro applies string value to biosource qualifier" Var Qualifier = %org.taxname% Value_To_Apply = "Homo sapiens" Handle_existing_text ="ePrepend" Delimiter = ":" Case_sensitive = false Ignore_space = true Ignore_punctuation = true For each BioSource Where EQUALS("org.common", Value_To_Apply, Case_sensitive, Ignore_space, Ignore_punctuation, "synonyms.txt", Value_To_Apply ) Do SetStringQual(Qualifier, Value_To_Apply, Handle_existing_text, Delimiter); Done ------------------------------------------------------------------------------ MACRO Autofix_macro_001 "Extend 3' end of feature to end of sequence for CDS features only objects that are 3' partial with 3' end no more than 2 from end of sequence and where sequence type is mRNA [cDNA]" FOR EACH Cdregion WHERE ISPARTIALSTOP("location") AND ISDISTFROMSTOP("location", "< 2") AND MOLINFO_FOR_SEQFEAT("biomol") = "mRNA" DO ExtendFeatToSeqStop(); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_002 "Extend 5' end of feature to end of sequence for CDS features only objects that are 5' partial with 5' end no more than 2 from end of sequence and where sequence type is mRNA [cDNA]" FOR EACH Cdregion WHERE ISPARTIALSTART("location") AND ISDISTFROMSTART("location", "< 2") AND MOLINFO_FOR_SEQFEAT("biomol") = "mRNA" DO ExtendFeatToSeqStart(); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_003 "Extend 3' end of feature to end of sequence for CDS features only objects that are 3' partial with 3' end no more than 2 from end of sequence and where source lineage contains 'Bacteria' (case-sensitive)" VAR case_sensitive = true FOR EACH Cdregion WHERE ISPARTIALSTOP("location") AND ISDISTFROMSTOP("location", "< 2") AND CONTAINS(BIOSOURCE_FOR_SEQFEAT("org.orgname.lineage"), "Bacteria", case_sensitive) DO ExtendFeatToSeqStop(); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_004 "Extend 5' end of feature to end of sequence for CDS features only objects that are 5' partial with 5' end no more than 2 from end of sequence and where source lineage contains 'Bacteria' (case-sensitive)" VAR case_sensitive = true FOR EACH Cdregion WHERE ISPARTIALSTART("location") AND ISDISTFROMSTART("location", "< 2") AND CONTAINS(BIOSOURCE_FOR_SEQFEAT("org.orgname.lineage"), "Bacteria", case_sensitive) DO ExtendFeatToSeqStart(); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_008 "Remove technique both where sequence type is protein and where technique is both" FOR EACH MolInfo WHERE biomol = "peptide" AND tech = "both" DO RemoveQual("tech"); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_009 "Synchronize coding region partials" FOR EACH Cdregion DO SynchronizeCDSPartials(); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_010 "Adjust coding regions for consensus splice sites" FOR EACH Cdregion DO AdjustCDSConsensusSpliceSites(); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_011 "Remove trailing * from complete coding regions" FOR EACH Cdregion DO TrimStopsFromCompleteCDS(); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_012 "Trim junk from primer (forward and reverse) sequences" VAR qual_name_fwd = "pcr-primers..forward..seq" qual_name_rev = "pcr-primers..reverse..seq" FOR EACH BioSource DO TrimJunkFromPrimerSeq(qual_name_fwd); TrimJunkFromPrimerSeq(qual_name_rev); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_013 "Remove seg-gaps" FOR EACH SeqAlign DO RemoveSegGaps(); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_014 "Edit taxname replace 'Human immunodeficiency virus-1' with 'Human immunodeficiency virus 1'" VAR qual_name = "org.taxname" find_text = "Human immunodeficiency virus-1" repl_text = "Human immunodeficiency virus 1" location = "anywhere" case_sensitive = true FOR EACH BioSource DO EditStringQual (qual_name, find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_015 "Edit taxname replace 'f.sp.' with 'f. sp.'" VAR qual_name = "org.taxname" find_text = "f.sp." repl_text = "f. sp." location = "anywhere" case_sensitive = false FOR EACH BioSource DO EditStringQual (qual_name, find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_016 "Edit taxname replace ' SP. ' with ' sp. '" VAR qual_name = "org.taxname" find_text = " SP. " repl_text = " sp. " location = "anywhere" case_sensitive = true FOR EACH BioSource DO EditStringQual (qual_name, find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_017 "Apply Homo sapiens to host (ignore new text when existing text is present) where source taxname starts with 'HIV' (case-sensitive)" VAR qual_name = "org.orgname.mod" modifier = "nat-host" new_value = "Homo sapiens" existing_text = "eLeaveOld" case_sensitive = true FOR EACH BioSource WHERE STARTS("org.taxname", "HIV", case_sensitive) DO obj = Resolve(qual_name) WHERE obj.subtype = modifier; SetModifier(obj, qual_name, modifier, new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_020 "Apply Homo sapiens to host (ignore new text when existing text is present) where source taxname starts with 'Human immunodeficiency virus' (ignore spaces, ignore punctuation)" VAR qual_name = "org.orgname.mod" modifier = "nat-host" new_value = "Homo sapiens" existing_text = "eLeaveOld" case_sensitive = false ignore_spaces = true ignore_punct = true FOR EACH BioSource WHERE STARTS("org.taxname", "Human immunodeficiency virus", case_sensitive, ignore_spaces, ignore_punct) DO obj = Resolve(qual_name) WHERE obj.subtype = modifier; SetModifier(obj, qual_name, modifier, new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_021 "Apply Homo sapiens to host (ignore new text when existing text is present) where source isolation-source equals 'Homo sapiens' (ignore spaces, ignore punctuation), allow 'Homo sapiens' to be replaced by 'human', 'Homo sapien', 'Homosapiens', 'Homo-sapiens', 'Homo spiens', 'Homo Sapience', 'homosapein', 'homosapiens', 'homosapien', 'homo_sapien', 'homo_sapiens', and 'Homosipian', allow 'sapiens' to be replaced by 'sapien', 'sapeins', 'sapein', 'sapins', 'sapens', 'sapin', 'sapen', 'sapians', 'sapian', 'sapies', and 'sapie' and where source taxname does not equal 'Homo sapiens' (case-sensitive)" VAR qual_name = "org.orgname.mod" modifier = "nat-host" new_value = "Homo sapiens" existing_text = "eLeaveOld" case_sensitiveA = false ignore_spaces = true ignore_punct = true case_sensitiveB = true FOR EACH BioSource WHERE EQUALS("subtype", "isolation-source", new_value, case_sensitiveA, ignore_spaces, ignore_punct, "synonyms.txt", new_value) AND NOT EQUALS("org.taxname", new_value, case_sensitiveB) DO obj = Resolve(qual_name) WHERE obj.subtype = modifier; SetModifier(obj, qual_name, modifier, new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_023 "Edit publication title replace ' ' with ''" VAR find_text = " " repl_text = "" location = "at the beginning" case_sensitive = true FOR EACH Pubdesc DO obj = PUB_TITLE("pub."); EditStringQual(obj, "", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_028 "Fix pub title where where title is all caps" FOR EACH Pubdesc DO obj = PUB_TITLE("pub.") WHERE ISUPPER(obj); FixPubCapsTitle(obj); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_029 "Fix pub title where where title is all lowercase" FOR EACH Pubdesc DO obj = PUB_TITLE("pub.") WHERE ISLOWER(obj); FixPubCapsTitle(obj); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_033 "Fix capitalization in author last names where last name is all caps" FOR EACH Pubdesc DO obj = PUB_AUTHORS("pub.", "last") WHERE ISUPPER(obj); FixCapsAuthorLastName(obj); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_034 "Fix pub affiliation country" FOR EACH Pubdesc DO obj = PUB_AFFIL("pub."); FixPubCapsAffilCountry(obj); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_035 "Fix pub affiliation (punctuation only)" Var punct_only = true FOR EACH Pubdesc DO obj = PUB_AFFIL("pub."); FixPubCapsAffiliation(obj, punct_only); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_036 "Remove publication state where state is all punctuation" FOR EACH Pubdesc DO obj = PUB_AFFIL("pub.", "sub") WHERE ISPUNCTUATION(obj); RemoveQual(obj); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_037 "Remove publication state where state contains 'Select A State' (ignore spaces, ignore punctuation), allow 'Select A State' to be replaced by 'none', 'N/A', 'Not Applicable', 'NotApplicable', 'Select State/Province', '--- Select One ---', 'N/A = Not Applicable', 'not USA', 'not USA/Canada', and 'outside of USA'" VAR match = "Select A State" case_sensitive = false ignore_space = true ignore_punctuation = true FOR EACH Pubdesc DO obj = PUB_AFFIL("pub.", "sub") WHERE CONTAINS(obj, match, case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", match); RemoveQual(obj); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_038 "Remove publication postal code where postal code is all punctuation" FOR EACH Pubdesc DO obj = PUB_AFFIL("pub.", "postal-code") WHERE ISPUNCTUATION(obj); RemoveQual(obj); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_039 "Remove publication postal code where postal code equals 'N/A' (ignore spaces, ignore punctuation), allow 'N/A' to be replaced by 'none', 'N.A.', and 'Not Applicable'" VAR match = "N/A" case_sensitive = false ignore_space = true ignore_punctuation = true FOR EACH Pubdesc DO obj = PUB_AFFIL("pub.", "postal-code") WHERE EQUALS(obj, match, case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", match); RemoveQual(obj); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_040 "Remove publication affiliation where affiliation is all punctuation" FOR EACH Pubdesc DO obj = PUB_AFFIL("pub.", "affil") WHERE ISPUNCTUATION(obj); RemoveQual(obj); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_041 "Remove publication affiliation where affiliation equals 'N/A', allow 'N/A' to be replaced by 'none', 'Not Applicable', and 'NotApplicable'" VAR match = "N/A" FOR EACH Pubdesc DO obj = PUB_AFFIL("pub.", "affil") WHERE EQUALS(obj, match, "synonyms.txt", match); RemoveQual(obj); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_042 "Remove publication department where department is all punctuation" FOR EACH Pubdesc DO obj = PUB_AFFIL("pub.", "div") WHERE ISPUNCTUATION(obj); RemoveQual(obj); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_043 "Remove publication department where department equals 'N/A', allow 'N/A' to be replaced by 'none', 'Not Applicable', and 'NotApplicable'" VAR match = "N/A" FOR EACH Pubdesc DO obj = PUB_AFFIL("pub.", "div") WHERE EQUALS(obj, match, "synonyms.txt", match); RemoveQual(obj); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_044 "Remove publication street where street is all punctuation" FOR EACH Pubdesc DO obj = PUB_AFFIL("pub.", "street") WHERE ISPUNCTUATION(obj); RemoveQual(obj); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_045 "Remove publication street where street equals 'N/A' (ignore spaces, ignore punctuation), allow 'N/A' to be replaced by 'none', 'Not Applicable', and 'NotApplicable'" VAR match = "N/A" case_sensitive = false ignore_space = true ignore_punctuation = true FOR EACH Pubdesc DO obj = PUB_AFFIL("pub.", "street") WHERE EQUALS(obj, match, case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", match); RemoveQual(obj); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_046 "Remove publication city where city is all punctuation" FOR EACH Pubdesc DO obj = PUB_AFFIL("pub.", "city") WHERE ISPUNCTUATION(obj); RemoveQual(obj); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_047 "Remove publication city where city equals 'N/A' (ignore spaces, ignore punctuation), allow 'N/A' to be replaced by 'none', 'Not Applicable', and 'NotApplicable'" VAR match = "N/A" case_sensitive = false ignore_space = true ignore_punctuation = true FOR EACH Pubdesc DO obj = PUB_AFFIL("pub.", "city") WHERE EQUALS(obj, match, case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", match); RemoveQual(obj); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_048 "Edit publication affiliation replace 'Sience' with 'Science'" VAR find_text = "Sience" repl_text = "Science" location = "anywhere" case_sensitive = true FOR EACH Pubdesc DO obj = PUB_AFFIL("pub.", "affil"); EditStringQual(obj, "", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_049 "Edit publication department replace 'Sience' with 'Science'" VAR find_text = "Sience" repl_text = "Science" location = "anywhere" case_sensitive = true FOR EACH Pubdesc DO obj = PUB_AFFIL("pub.", "div"); EditStringQual(obj, "", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_050 "Edit publication street replace 'Sience' with 'Science'" VAR find_text = "Sience" repl_text = "Science" location = "anywhere" case_sensitive = true FOR EACH Pubdesc DO obj = PUB_AFFIL("pub.", "street"); EditStringQual(obj, "", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_051 "Fix pub title where where title is all caps" FOR EACH Pubdesc DO obj = PUB_TITLE("pub.") WHERE ISUPPER(obj); FixPubCapsTitle(obj); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_052 "Edit publication title replace ' sp' with ' sp..'" VAR find_text = " sp" repl_text = " sp.." location = "at the end" case_sensitive = true FOR EACH Pubdesc DO obj = PUB_TITLE("pub."); EditStringQual(obj, "", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_053 "Edit publication title replace ' sp.' with ' sp..'" VAR find_text = " sp." repl_text = " sp.." location = "at the end" case_sensitive = true FOR EACH Pubdesc DO obj = PUB_TITLE("pub."); EditStringQual(obj, "", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_054 "Edit publication title replace ' spp' with ' spp..'" VAR find_text = " spp" repl_text = " spp.." location = "at the end" case_sensitive = true FOR EACH Pubdesc DO obj = PUB_TITLE("pub."); EditStringQual(obj, "", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_055 "Edit publication title replace ' spp.' with ' spp..'" VAR find_text = " spp." repl_text = " spp.." location = "at the end" case_sensitive = true FOR EACH Pubdesc DO obj = PUB_TITLE("pub."); EditStringQual(obj, "", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_056 "Edit publication title replace '#' with ' '" VAR find_text = "#" repl_text = " " location = "anywhere" case_sensitive = true FOR EACH Pubdesc DO obj = PUB_TITLE("pub."); EditStringQual(obj, "", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_057 "Edit publication title replace ' ' with ''" VAR find_text = " " repl_text = "" location = "at the beginning" case_sensitive = true FOR EACH Pubdesc DO obj = PUB_TITLE("pub."); EditStringQual(obj, "", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_061 "Apply Homo sapiens to host (overwrite existing text) where source host equals 'homo sapiens' (ignore spaces, ignore punctuation), allow 'homo sapiens' to be replaced by 'humans', 'human', 'Homo sapien', 'Homosapiens', 'Homo-sapiens', 'Homo spiens', 'Homo Sapience', 'Homo sappiens', and 'homo_sapien', allow 'sapiens' to be replaced by 'sapeins', 'sapein', 'sapens', 'sapins', 'sapin', 'sapen', 'spaeins', 'sapians', 'sapian', 'sapies', and 'sapie'" VAR qual_name = "org.orgname.mod" modifier = "nat-host" new_value = "Homo sapiens" existing_text = "eReplace" case_sensitive = true ignore_spaces = true ignore_punct = true FOR EACH BioSource WHERE EQUALS(qual_name, modifier, "homo sapiens", case_sensitive, ignore_spaces, ignore_punct, "synonyms.txt", "homo sapiens") DO obj = Resolve(qual_name) WHERE obj.subtype = modifier; SetModifier(obj, qual_name, modifier, new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_065 "Edit isolation-source replace 'faeces' (case insensitive) with 'feces'" VAR find_text = "faeces" repl_text = "feces" location = "anywhere" case_sensitive = false FOR EACH BioSource DO o = Resolve("subtype") WHERE o.subtype = "isolation-source"; EditStringQual (o, "name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_066 "Edit isolation-source replace 'faecal' with 'fecal'" VAR find_text = "faecal" repl_text = "fecal" location = "anywhere" case_sensitive = true FOR EACH BioSource DO o = Resolve("subtype") WHERE o.subtype = "isolation-source"; EditStringQual (o, "name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_067 "Edit country replace '`' with '''" VAR find_text = "`" repl_text = "'" location = "anywhere" case_sensitive = true FOR EACH BioSource DO o = Resolve("subtype") WHERE o.subtype = "country"; EditStringQual (o, "name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_068 "Apply Virgin Islands to country (overwrite existing text) where source country equals 'US Virgin Islands' (ignore spaces, ignore punctuation), allow 'US Virgin Islands' to be replaced by 'U.S. Virgin Islands' and 'United States Virgin Islands'" VAR qual_name = "subtype" modifier = "country" new_value = "Virgin Islands" existing_text = "eReplace" case_sensitive = false ignore_spaces = true ignore_punct = true FOR EACH BioSource WHERE EQUALS("subtype", "country", "US Virgin Islands", case_sensitive, ignore_spaces, ignore_punct,"synonyms.txt", "US Virgin Islands") DO obj = Resolve(qual_name) WHERE obj.subtype = modifier; SetModifier(obj, qual_name, modifier, new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_069 "Edit country replace 'Cote d' Ivoire' (case insensitive) with 'Cote d'Ivoire'" VAR find_text = "Cote d' Ivoire" repl_text = "Cote d'Ivoire" location = "anywhere" case_sensitive = false FOR EACH BioSource DO o = Resolve("subtype") WHERE o.subtype = "country"; EditStringQual (o, "name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_070 "Edit country replace 'Coted'Ivoire' (case insensitive) with 'Cote d'Ivoire'" VAR find_text = "Coted'Ivoire" repl_text = "Cote d'Ivoire" location = "anywhere" case_sensitive = false FOR EACH BioSource DO o = Resolve("subtype") WHERE o.subtype = "country"; EditStringQual (o, "name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_071 "Edit country replace 'Guinea Bissau' (case insensitive) with 'Guinea-Bissau'" VAR find_text = "Guinea Bissau" repl_text = "Guinea-Bissau" location = "anywhere" case_sensitive = false FOR EACH BioSource DO o = Resolve("subtype") WHERE o.subtype = "country"; EditStringQual (o, "name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_072 "Edit country replace 'Guinea_Bissau' (case insensitive) with 'Guinea-Bissau'" VAR find_text = "Guinea_Bissau" repl_text = "Guinea-Bissau" location = "anywhere" case_sensitive = false FOR EACH BioSource DO o = Resolve("subtype") WHERE o.subtype = "country"; EditStringQual (o, "name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_073 "Edit country replace 'GuineaBissau' (case insensitive) with 'Guinea-Bissau'" VAR find_text = "GuineaBissau" repl_text = "Guinea-Bissau" location = "anywhere" case_sensitive = false FOR EACH BioSource DO o = Resolve("subtype") WHERE o.subtype = "country"; EditStringQual (o, "name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_074 "Edit country replace 'Scotland' (case insensitive) with 'United Kingdom: Scotland' where source country equals 'Scotland' (ignore punctuation)" VAR find_text = "Scotland" repl_text = "United Kingdom: Scotland" location = "at the beginning" case_sensitive = false ignore_spaces = false ignore_punct = true FOR EACH BioSource WHERE EQUALS("subtype", "country", find_text, case_sensitive, ignore_spaces, ignore_punct) DO o = Resolve("subtype") WHERE o.subtype = "country"; EditStringQual (o, "name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_075 "Edit country replace 'Wales' (case insensitive) with 'United Kingdom: Wales' where source country equals 'Wales' (ignore punctuation)" VAR find_text = "Wales" repl_text = "United Kingdom: Wales" location = "at the beginning" case_sensitive = false ignore_spaces = false ignore_punct = true FOR EACH BioSource WHERE EQUALS("subtype", "country", find_text, case_sensitive, ignore_spaces, ignore_punct) DO o = Resolve("subtype") WHERE o.subtype = "country"; EditStringQual (o, "name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_076 "Edit country replace 'Democratic People's Republic of Korea' (case insensitive) with 'North Korea' where source country equals 'Democratic People's Republic of Korea' (ignore spaces, ignore punctuation)" VAR find_text = "Democratic People's Republic of Korea" repl_text = "North Korea" location = "at the beginning" case_sensitive = false ignore_spaces = true ignore_punct = true FOR EACH BioSource WHERE EQUALS("subtype", "country", find_text, case_sensitive, ignore_spaces, ignore_punct) DO o = Resolve("subtype") WHERE o.subtype = "country"; EditStringQual (o, "name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_077 "Edit country replace 'Republic of Korea' (case insensitive) with 'South Korea' where source country equals 'Republic of Korea' (ignore spaces, ignore punctuation)" VAR find_text = "Republic of Korea" repl_text = "South Korea" location = "at the beginning" case_sensitive = false ignore_spaces = true ignore_punct = true FOR EACH BioSource WHERE EQUALS("subtype", "country", find_text, case_sensitive, ignore_spaces, ignore_punct) DO o = Resolve("subtype") WHERE o.subtype = "country"; EditStringQual (o, "name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_078 "Edit country replace 'Russian Federation' (case insensitive) with 'Russia' where source country equals 'Russian Federation' (ignore spaces, ignore punctuation)" VAR find_text = "Russian Federation" repl_text = "Russia" location = "at the beginning" case_sensitive = false ignore_spaces = true ignore_punct = true FOR EACH BioSource WHERE EQUALS("subtype", "country", find_text, case_sensitive, ignore_spaces, ignore_punct) DO o = Resolve("subtype") WHERE o.subtype = "country"; EditStringQual (o, "name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_079 "Fix source country qualifier capitalization" For each BioSource Do o = Resolve("subtype") Where o.subtype = "country"; FixSourceQualCaps(o, "name"); Done ------------------------------------------------------------------------------ MACRO Autofix_macro_080 "Fix capitalization in sex source qualifier" For each BioSource Do o = Resolve("subtype") Where o.subtype = "sex"; FixSourceQualCaps(o, "name"); Done ------------------------------------------------------------------------------ MACRO Autofix_macro_081 "Fix capitalization in host source qualifier" For each BioSource Do o = Resolve("org.orgname.mod") Where o.subtype = "nat-host"; FixSourceQualCaps(o, "name"); Done ------------------------------------------------------------------------------ MACRO Autofix_macro_082 "Fix capitalization in isolation-source source qualifier" For each BioSource Do o = Resolve("subtype") Where o.subtype = "isolation-source"; FixSourceQualCaps(o, "name"); Done ------------------------------------------------------------------------------ MACRO Autofix_macro_083 "Fix capitalization in dev-stage source qualifier" For each BioSource Do o = Resolve("subtype") Where o.subtype = "dev-stage"; FixSourceQualCaps(o, "name"); Done ------------------------------------------------------------------------------ MACRO Autofix_macro_084 "Fix capitalization in tissue-type source qualifier" For each BioSource Do o = Resolve("subtype") Where o.subtype = "tissue-type"; FixSourceQualCaps(o, "name"); Done ------------------------------------------------------------------------------ MACRO Autofix_macro_085 "Fix capitalization in lab-host source qualifier" For each BioSource Do o = Resolve("subtype") Where o.subtype = "lab-host"; FixSourceQualCaps(o, "name"); Done ------------------------------------------------------------------------------ MACRO Autofix_macro_086 "Fix capitalization in cell-type source qualifier" For each BioSource Do o = Resolve("subtype") Where o.subtype = "cell-type"; FixSourceQualCaps(o, "name"); Done ------------------------------------------------------------------------------ MACRO Autofix_macro_088 "Fix collection-date format" For each BioSource Do o = Resolve("subtype") Where o.subtype = "collection-date"; FixFormat(o); Done ------------------------------------------------------------------------------ MACRO Autofix_macro_089 "Edit segment replace 'segment-' (case insensitive) with ''" VAR find_text = "segment-" repl_text = "" location = "at the beginning" case_sensitive = false FOR EACH BioSource DO o = Resolve("subtype") WHERE o.subtype = "segment"; EditStringQual (o, "name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_090 "Edit segment replace 'segment_' (case insensitive) with ''" VAR find_text = "segment_" repl_text = "" location = "at the beginning" case_sensitive = false FOR EACH BioSource DO o = Resolve("subtype") WHERE o.subtype = "segment"; EditStringQual (o, "name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_091 "Edit segment replace 'segment:' (case insensitive) with ''" VAR find_text = "segment:" repl_text = "" location = "at the beginning" case_sensitive = false FOR EACH BioSource DO o = Resolve("subtype") WHERE o.subtype = "segment"; EditStringQual (o, "name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_092 "Edit segment replace 'segment' (case insensitive) with ''" VAR find_text = "segment" repl_text = "" location = "anywhere" case_sensitive = false FOR EACH BioSource DO o = Resolve("subtype") WHERE o.subtype = "segment"; EditStringQual (o, "name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_093 "Edit strain replace 'strain-' (case insensitive) with ''" VAR find_text = "strain-" repl_text = "" location = "at the beginning" case_sensitive = false FOR EACH BioSource DO o = Resolve("org.orgname.mod") WHERE o.subtype = "strain"; EditStringQual (o, "subname", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_094 "Edit strain replace 'strain_' (case insensitive) with ''" VAR find_text = "strain_" repl_text = "" location = "at the beginning" case_sensitive = false FOR EACH BioSource DO o = Resolve("org.orgname.mod") WHERE o.subtype = "strain"; EditStringQual (o, "subname", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_095 "Edit strain replace 'strain:' (case insensitive) with ''" VAR find_text = "strain:" repl_text = "" location = "at the beginning" case_sensitive = false FOR EACH BioSource DO o = Resolve("org.orgname.mod") WHERE o.subtype = "strain"; EditStringQual (o, "subname", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_096 "Edit strain replace 'strain' (case insensitive) with '' where source strain does not contain 'strains' (ignore spaces, ignore punctuation)" VAR find_text = "strain" repl_text = "" location = "at the beginning" case_sensitive = false ignore_spaces = true ignore_punct = true FOR EACH BioSource WHERE NOT CONTAINS("org.orgname.mod", "strain", "strains", case_sensitive, ignore_spaces, ignore_punct) DO o = Resolve("org.orgname.mod") WHERE o.subtype = "strain"; EditStringQual (o, "subname", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_097 "Edit strain replace ' strain' (case insensitive) with '' where source strain does not contain 'strains' (ignore spaces, ignore punctuation)" VAR find_text = " strain" repl_text = "" location = "at the end" case_sensitive = false ignore_spaces = true ignore_punct = true FOR EACH BioSource WHERE NOT CONTAINS("org.orgname.mod", "strain", "strains", case_sensitive, ignore_spaces, ignore_punct) DO o = Resolve("org.orgname.mod") WHERE o.subtype = "strain"; EditStringQual (o, "subname", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_098 "Edit clone replace 'clone-' (case insensitive) with ''" VAR find_text = "clone-" repl_text = "" location = "at the beginning" case_sensitive = false FOR EACH BioSource DO o = Resolve("subtype") WHERE o.subtype = "clone"; EditStringQual (o, "name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_099 "Edit clone replace 'clone_' (case insensitive) with ''" VAR find_text = "clone_" repl_text = "" location = "at the beginning" case_sensitive = false FOR EACH BioSource DO o = Resolve("subtype") WHERE o.subtype = "clone"; EditStringQual (o, "name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_100 "Edit clone replace 'clone:' (case insensitive) with ''" VAR find_text = "clone:" repl_text = "" location = "at the beginning" case_sensitive = false FOR EACH BioSource DO o = Resolve("subtype") WHERE o.subtype = "clone"; EditStringQual (o, "name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_101 "Edit clone replace 'clone' (case insensitive) with ''" VAR find_text = "clone" repl_text = "" location = "at the beginning" case_sensitive = false FOR EACH BioSource DO o = Resolve("subtype") WHERE o.subtype = "clone"; EditStringQual (o, "name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_102 "Edit clone replace 'clone' (case insensitive) with ''" VAR find_text = "clone" repl_text = "" location = "at the end" case_sensitive = false FOR EACH BioSource DO o = Resolve("subtype") WHERE o.subtype = "clone"; EditStringQual (o, "name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_103 "Edit isolate replace 'isolate-' (case insensitive) with ''" VAR find_text = "isolate-" repl_text = "" location = "at the beginning" case_sensitive = false FOR EACH BioSource DO o = Resolve("org.orgname.mod") WHERE o.subtype = "isolate"; EditStringQual (o, "subname", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_104 "Edit isolate replace 'isolate_' (case insensitive) with ''" VAR find_text = "isolate_" repl_text = "" location = "at the beginning" case_sensitive = false FOR EACH BioSource DO o = Resolve("org.orgname.mod") WHERE o.subtype = "isolate"; EditStringQual (o, "subname", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_105 "Edit isolate replace 'isolate:' (case insensitive) with ''" VAR find_text = "isolate:" repl_text = "" location = "at the beginning" case_sensitive = false FOR EACH BioSource DO o = Resolve("org.orgname.mod") WHERE o.subtype = "isolate"; EditStringQual (o, "subname", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_106 "Edit isolate replace 'isolate' (case insensitive) with '' where source isolate does not contain 'isolated' (ignore spaces, ignore punctuation)" VAR find_text = "isolate" repl_text = "" location = "at the beginning" case_sensitive = false ignore_spaces = true ignore_punct = true FOR EACH BioSource WHERE NOT CONTAINS("org.orgname.mod", "isolate", "isolated", case_sensitive, ignore_spaces, ignore_punct) DO o = Resolve("org.orgname.mod") WHERE o.subtype = "isolate"; EditStringQual (o, "subname", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_107 "Edit isolate replace 'isolate' (case insensitive) with '' where source isolate does not contain 'isolated' (ignore spaces, ignore punctuation)" VAR find_text = "isolate" repl_text = "" location = "at the end" case_sensitive = false ignore_spaces = true ignore_punct = true FOR EACH BioSource WHERE NOT CONTAINS("org.orgname.mod", "isolate", "isolated", case_sensitive, ignore_spaces, ignore_punct) DO o = Resolve("org.orgname.mod") WHERE o.subtype = "isolate"; EditStringQual (o, "subname", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_108 "Remove location nucleomorph where source dbxref starts with 'taxon:' (case-sensitive) and where source division is present and where source lineage is present and where source lineage does not contain 'Chlorarachniophyceae' (case-sensitive) and where source lineage does not contain 'Cryptophyta' (case-sensitive)" VAR match_field = "org.orgname.lineage" match_text1 = "Chlorarachniophyceae" match_text2 = "Cryptophyta" case_sensitive = true FOR EACH BioSource WHERE genome = "nucleomorph" AND STARTS("org.db.db", "taxon", case_sensitive) AND ISPRESENT("org.orgname.div") AND ISPRESENT(match_field) AND NOT CONTAINS(match_field, match_text1, case_sensitive) AND NOT CONTAINS(match_field, match_text2, case_sensitive) Do RemoveQual("genome"); Done ------------------------------------------------------------------------------ MACRO Autofix_macro_109 "Remove note-orgmod where source note-orgmod equals 'Organelle: nucleomorph' and where source dbxref starts with 'taxon:' (case-sensitive) and where source division is present and where source lineage is present and where source lineage does not contain 'Chlorarachniophyceae' (case-sensitive) and where source lineage does not contain 'Cryptophyta' (case-sensitive)" VAR match_field = "org.orgname.lineage" match_text1 = "Chlorarachniophyceae" match_text2 = "Cryptophyta" case_sensitive = true FOR EACH BioSource WHERE STARTS("org.db.db", "taxon", case_sensitive) AND ISPRESENT("org.orgname.div") AND ISPRESENT(match_field) AND NOT CONTAINS(match_field, match_text1, case_sensitive) AND NOT CONTAINS(match_field, match_text2, case_sensitive) DO obj = Resolve("org.orgname.mod") WHERE obj.subtype = "other" AND obj.subname = "Organelle: nucleomorph"; RemoveModifier(obj); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_110 "Remove note-orgmod where source note-orgmod equals 'nucleomorph' and where source dbxref starts with 'taxon:' (case-sensitive) and where source division is present and where source lineage is present and where source lineage does not contain 'Chlorarachniophyceae' (case-sensitive) and where source lineage does not contain 'Cryptophyta' (case-sensitive)" VAR match_field = "org.orgname.lineage" match_text1 = "Chlorarachniophyceae" match_text2 = "Cryptophyta" case_sensitive = true FOR EACH BioSource WHERE STARTS("org.db.db", "taxon", case_sensitive) AND ISPRESENT("org.orgname.div") AND ISPRESENT(match_field) AND NOT CONTAINS(match_field, match_text1, case_sensitive) AND NOT CONTAINS(match_field, match_text2, case_sensitive) DO obj = Resolve("org.orgname.mod") WHERE obj.subtype = "other" AND obj.subname = "nucleomorph"; RemoveModifier(obj); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_111 "Remove note-subsrc where source note-subsrc equals 'Organelle: nucleomorph' and where source dbxref starts with 'taxon:' (case-sensitive) and where source division is present and where source lineage is present and where source lineage does not contain 'Chlorarachniophyceae' (case-sensitive) and where source lineage does not contain 'Cryptophyta' (case-sensitive)" VAR match_field = "org.orgname.lineage" match_text1 = "Chlorarachniophyceae" match_text2 = "Cryptophyta" case_sensitive = true FOR EACH BioSource WHERE STARTS("org.db.db", "taxon", case_sensitive) AND ISPRESENT("org.orgname.div") AND ISPRESENT(match_field) AND NOT CONTAINS(match_field, match_text1, case_sensitive) AND NOT CONTAINS(match_field, match_text2, case_sensitive) DO obj = Resolve("subtype") WHERE obj.subtype = "other" AND obj.name = "Organelle: nucleomorph"; RemoveModifier(obj); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_112 "Remove note-subsrc where source note-subsrc equals 'nucleomorph' and where source dbxref starts with 'taxon:' (case-sensitive) and where source division is present and where source lineage is present and where source lineage does not contain 'Chlorarachniophyceae' (case-sensitive) and where source lineage does not contain 'Cryptophyta' (case-sensitive)" VAR match_field = "org.orgname.lineage" match_text1 = "Chlorarachniophyceae" match_text2 = "Cryptophyta" case_sensitive = true FOR EACH BioSource WHERE STARTS("org.db.db", "taxon", case_sensitive) AND ISPRESENT("org.orgname.div") AND ISPRESENT(match_field) AND NOT CONTAINS(match_field, match_text1, case_sensitive) AND NOT CONTAINS(match_field, match_text2, case_sensitive) DO obj = Resolve("subtype") WHERE obj.subtype = "other" AND obj.name = "nucleomorph"; RemoveModifier(obj); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_113 "Remove location macronuclear where source dbxref starts with 'taxon:' (case-sensitive) and where source division is present and where source lineage is present and where source lineage does not contain 'Ciliophora' (case-sensitive)" VAR match_field = "org.orgname.lineage" match_text = "Ciliophora" case_sensitive = true FOR EACH BioSource WHERE genome = "macronuclear" AND STARTS("org.db.db", "taxon", case_sensitive) AND ISPRESENT("org.orgname.div") AND ISPRESENT(match_field) AND NOT CONTAINS(match_field, match_text, case_sensitive) Do RemoveQual("genome"); Done ------------------------------------------------------------------------------ MACRO Autofix_macro_114 "Remove note-orgmod where source note-orgmod equals 'Organelle: macronuclear' and where source dbxref starts with 'taxon:' (case-sensitive) and where source division is present and where source lineage is present and where source lineage does not contain 'Ciliophora' (case-sensitive)" VAR match_field = "org.orgname.lineage" match_text = "Ciliophora" case_sensitive = true FOR EACH BioSource WHERE STARTS("org.db.db", "taxon", case_sensitive) AND ISPRESENT("org.orgname.div") AND ISPRESENT(match_field) AND NOT CONTAINS(match_field, match_text, case_sensitive) DO obj = Resolve("org.orgname.mod") WHERE obj.subtype = "other" AND obj.subname = "Organelle: macronuclear"; RemoveModifier(obj); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_115 "Remove note-orgmod where source note-orgmod equals 'macronuclear' and where source dbxref starts with 'taxon:' (case-sensitive) and where source division is present and where source lineage is present and where source lineage does not contain 'Ciliophora' (case-sensitive)" VAR match_field = "org.orgname.lineage" match_text = "Ciliophora" case_sensitive = true FOR EACH BioSource WHERE STARTS("org.db.db", "taxon", case_sensitive) AND ISPRESENT("org.orgname.div") AND ISPRESENT(match_field) AND NOT CONTAINS(match_field, match_text, case_sensitive) DO obj = Resolve("org.orgname.mod") WHERE obj.subtype = "other" AND obj.subname = "macronuclear"; RemoveModifier(obj); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_116 "Remove note-subsrc where source note-subsrc equals 'Organelle: macronuclear' and where source dbxref starts with 'taxon:' (case-sensitive) and where source division is present and where source lineage is present and where source lineage does not contain 'Ciliophora' (case-sensitive)" VAR match_field = "org.orgname.lineage" match_text = "Ciliophora" case_sensitive = true FOR EACH BioSource WHERE STARTS("org.db.db", "taxon", case_sensitive) AND ISPRESENT("org.orgname.div") AND ISPRESENT(match_field) AND NOT CONTAINS(match_field, match_text, case_sensitive) DO obj = Resolve("subtype") WHERE obj.subtype = "other" AND obj.name = "Organelle: macronuclear"; RemoveModifier(obj); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_117 "Remove note-subsrc where source note-subsrc equals 'macronuclear' and where source dbxref starts with 'taxon:' (case-sensitive) and where source division is present and where source lineage is present and where source lineage does not contain 'Ciliophora' (case-sensitive)" VAR match_field = "org.orgname.lineage" match_text = "Ciliophora" case_sensitive = true FOR EACH BioSource WHERE STARTS("org.db.db", "taxon", case_sensitive) AND ISPRESENT("org.orgname.div") AND ISPRESENT(match_field) AND NOT CONTAINS(match_field, match_text, case_sensitive) DO obj = Resolve("subtype") WHERE obj.subtype = "other" AND obj.name = "macronuclear"; RemoveModifier(obj); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_119 "Fix lat-lon format" FOR EACH BioSource DO obj = Resolve("subtype") Where obj.subtype = "lat-lon"; FixFormat(obj); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_122 "Edit CDS note replace '[intronless gene]' with '' where source lineage starts with 'Bacteria' (case-sensitive)" VAR find_text = "[intronless gene]" repl_text = "" location = "anywhere" case_sensitive = true FOR EACH Cdregion WHERE STARTS(BIOSOURCE_FOR_SEQFEAT("org.orgname.lineage"), "Bacteria", case_sensitive) DO EditStringQual("comment", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_123 "Edit CDS note replace '[intronless gene]' with '' where source lineage starts with 'Viruses' (case-sensitive)" VAR find_text = "[intronless gene]" repl_text = "" location = "anywhere" case_sensitive = true FOR EACH Cdregion WHERE STARTS(BIOSOURCE_FOR_SEQFEAT("org.orgname.lineage"), "Viruses", case_sensitive) DO EditStringQual("comment", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_124 "Edit CDS note replace '[intronless gene]' with '' where source lineage starts with 'Archaea' (case-sensitive)" VAR find_text = "[intronless gene]" repl_text = "" location = "anywhere" case_sensitive = true FOR EACH Cdregion WHERE STARTS(BIOSOURCE_FOR_SEQFEAT("org.orgname.lineage"), "Archaea", case_sensitive) DO EditStringQual("comment", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_125 "Edit CDS note replace '[intronless gene]' with '' where sequence type is mRNA [cDNA]" VAR find_text = "[intronless gene]" repl_text = "" location = "anywhere" case_sensitive = true FOR EACH Cdregion WHERE MOLINFO_FOR_SEQFEAT("biomol") = "mRNA" DO EditStringQual("comment", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_136 "Edit strain replace 'ATCC:' with 'ATCC '" VAR find_text = "ATCC:" repl_text = "ATCC " location = "anywhere" case_sensitive = true FOR EACH BioSource DO o = Resolve("org.orgname.mod") WHERE o.subtype = "strain"; EditStringQual (o, "subname", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_137 "Edit cell-line replace 'ATCC:' with 'ATCC '" VAR find_text = "ATCC:" repl_text = "ATCC " location = "anywhere" case_sensitive = true FOR EACH BioSource DO o = Resolve("subtype") WHERE o.subtype = "cell-line"; EditStringQual (o, "name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_138 "Edit tissue-type replace 'ATCC:' with 'ATCC '" VAR find_text = "ATCC:" repl_text = "ATCC " location = "anywhere" case_sensitive = true FOR EACH BioSource DO o = Resolve("subtype") WHERE o.subtype = "tissue-type"; EditStringQual (o, "name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_139 "Edit strain replace 'CBS:' with 'CBS '" VAR find_text = "CBS:" repl_text = "CBS " location = "anywhere" case_sensitive = true FOR EACH BioSource DO o = Resolve("org.orgname.mod") WHERE o.subtype = "strain"; EditStringQual (o, "subname", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_140 "Edit strain replace 'DSMZ:' with 'DSMZ '" VAR find_text = "DSMZ:" repl_text = "DSMZ " location = "anywhere" case_sensitive = true FOR EACH BioSource DO o = Resolve("org.orgname.mod") WHERE o.subtype = "strain"; EditStringQual (o, "subname", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_141 "Edit strain replace 'DSM:' with 'DSM '" VAR find_text = "DSM:" repl_text = "DSM " location = "anywhere" case_sensitive = true FOR EACH BioSource DO o = Resolve("org.orgname.mod") WHERE o.subtype = "strain"; EditStringQual (o, "subname", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_142 "Edit strain replace 'ATCC' with 'ATCC ' where source strain does not contain 'ATCC ' (case-sensitive) and where source strain does not equal 'ATCC'" VAR find_text = "ATCC" repl_text = "ATCC " location = "anywhere" case_sensitive = true FOR EACH BioSource WHERE NOT CONTAINS("org.orgname.mod", "strain", repl_text, case_sensitive) AND NOT EQUALS("org.orgname.mod", "strain", find_text) DO o = Resolve("org.orgname.mod") WHERE o.subtype = "strain"; EditStringQual (o, "subname", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_143 "Edit cell-line replace 'ATCC' with 'ATCC ' where source strain does not contain 'ATCC ' (case-sensitive) and where source strain does not equal 'ATCC'" VAR find_text = "ATCC" repl_text = "ATCC " location = "anywhere" case_sensitive = true FOR EACH BioSource WHERE NOT CONTAINS("org.orgname.mod", "strain", repl_text, case_sensitive) AND NOT EQUALS("org.orgname.mod", "strain", find_text) DO o = Resolve("subtype") WHERE o.subtype = "cell-line"; EditStringQual (o, "name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_144 "Edit tissue-type replace 'ATCC' with 'ATCC ' where source strain does not contain 'ATCC ' (case-sensitive) and where source strain does not equal 'ATCC'" VAR find_text = "ATCC" repl_text = "ATCC " location = "anywhere" case_sensitive = true FOR EACH BioSource WHERE NOT CONTAINS("org.orgname.mod", "strain", repl_text, case_sensitive) AND NOT EQUALS("org.orgname.mod", "strain", find_text) DO o = Resolve("subtype") WHERE o.subtype = "tissue-type"; EditStringQual (o, "name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_145 "Edit strain replace 'CBS' with 'CBS ' where source strain does not contain 'CBS ' (case-sensitive) and where source strain does not equal 'CBS'" VAR find_text = "CBS" repl_text = "CBS " location = "anywhere" case_sensitive = true FOR EACH BioSource WHERE NOT CONTAINS("org.orgname.mod", "strain", repl_text, case_sensitive) AND NOT EQUALS("org.orgname.mod", "strain", find_text) DO o = Resolve("org.orgname.mod") WHERE o.subtype = "strain"; EditStringQual (o, "subname", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_146 "Edit strain replace 'DSMZ' with 'DSMZ ' where source strain does not contain 'DSMZ ' (case-sensitive) and where source strain does not equal 'DSMZ'" VAR find_text = "DSMZ" repl_text = "DSMZ " location = "anywhere" case_sensitive = true FOR EACH BioSource WHERE NOT CONTAINS("org.orgname.mod", "strain", repl_text, case_sensitive) AND NOT EQUALS("org.orgname.mod", "strain", find_text) DO o = Resolve("org.orgname.mod") WHERE o.subtype = "strain"; EditStringQual (o, "subname", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_147 "Edit strain replace 'DSM' with 'DSM ' where source strain does not contain 'DSM ' (case-sensitive) and where source strain does not equal 'DSM' and where source strain does not contain 'DSMZ' (case-sensitive)" VAR find_text = "DSM" repl_text = "DSM " location = "anywhere" case_sensitive = true FOR EACH BioSource WHERE NOT CONTAINS("org.orgname.mod", "strain", repl_text, case_sensitive) AND NOT EQUALS("org.orgname.mod", "strain", find_text) AND NOT CONTAINS("org.orgname.mod", "strain", "DSMZ", case_sensitive) DO o = Resolve("org.orgname.mod") WHERE o.subtype = "strain"; EditStringQual (o, "subname", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_148 "Fix i in primer (forward and reverse) sequences" VAR qual_name_fwd = "pcr-primers..forward..seq" qual_name_rev = "pcr-primers..reverse..seq" FOR EACH BioSource DO FixIInPrimerSeq(qual_name_fwd); FixIInPrimerSeq(qual_name_rev); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_149 "Fix USA and state abbreviations in publications" FOR EACH Pubdesc DO FixUSAAndStateAbbreviations(); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_150 "Remove lineage source notes" FOR EACH BioSource DO RemoveLineageSourceNotes(); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_154 "Edit isolate replace 'GGE_gel_band_' with 'GGE gel band '" VAR find_text = "GGE_gel_band_" repl_text = "GGE gel band " location = "anywhere" case_sensitive = true FOR EACH BioSource DO o = Resolve("org.orgname.mod") WHERE o.subtype = "isolate"; EditStringQual (o, "subname", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_155 "Edit isolate replace 'GGE_gel_band' with 'GGE gel band'" VAR find_text = "GGE_gel_band" repl_text = "GGE gel band" location = "anywhere" case_sensitive = true FOR EACH BioSource DO o = Resolve("org.orgname.mod") WHERE o.subtype = "isolate"; EditStringQual (o, "subname", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_156 "Edit isolate replace 'GGEgelband' with 'GGE gel band'" VAR find_text = "GGEgelband" repl_text = "GGE gel band" location = "anywhere" case_sensitive = true FOR EACH BioSource DO o = Resolve("org.orgname.mod") WHERE o.subtype = "isolate"; EditStringQual (o, "subname", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_157 "Edit isolate replace 'GGEband' with 'GGE gel band' where source isolate does not contain 'gel'" VAR find_text = "GGEband" repl_text = "GGE gel band" location = "anywhere" case_sensitive = true FOR EACH BioSource WHERE NOT CONTAINS("org.orgname.mod", "isolate", "gel") DO o = Resolve("org.orgname.mod") WHERE o.subtype = "isolate"; EditStringQual (o, "subname", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_158 "Edit isolate replace 'GGE-band' with 'GGE gel band' where source isolate does not contain 'gel'" VAR find_text = "GGE-band" repl_text = "GGE gel band" location = "anywhere" case_sensitive = true FOR EACH BioSource WHERE NOT CONTAINS("org.orgname.mod", "isolate", "gel") DO o = Resolve("org.orgname.mod") WHERE o.subtype = "isolate"; EditStringQual (o, "subname", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_159 "Edit isolate replace 'GGE-gel band' with 'GGE gel band'" VAR find_text = "GGE-gel band" repl_text = "GGE gel band" location = "anywhere" case_sensitive = true FOR EACH BioSource DO o = Resolve("org.orgname.mod") WHERE o.subtype = "isolate"; EditStringQual (o, "subname", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_160 "Edit isolate replace 'GGE_gel_' with 'GGE gel band ' where source isolate does not contain 'band'" VAR find_text = "GGE_gel_" repl_text = "GGE gel band " location = "anywhere" case_sensitive = true FOR EACH BioSource WHERE NOT CONTAINS("org.orgname.mod", "isolate", "band") DO o = Resolve("org.orgname.mod") WHERE o.subtype = "isolate"; EditStringQual (o, "subname", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_161 "Edit isolate replace 'GGE_gel' with 'GGE gel band' where source isolate does not contain 'band'" VAR find_text = "GGE_gel" repl_text = "GGE gel band" location = "anywhere" case_sensitive = true FOR EACH BioSource WHERE NOT CONTAINS("org.orgname.mod", "isolate", "band") DO o = Resolve("org.orgname.mod") WHERE o.subtype = "isolate"; EditStringQual (o, "subname", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_162 "Edit isolate replace 'GGE_band_' with 'GGE gel band ' where source isolate does not contain 'gel'" VAR find_text = "GGE_band_" repl_text = "GGE gel band " location = "anywhere" case_sensitive = true FOR EACH BioSource WHERE NOT CONTAINS("org.orgname.mod", "isolate", "gel") DO o = Resolve("org.orgname.mod") WHERE o.subtype = "isolate"; EditStringQual (o, "subname", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_163 "Edit isolate replace 'GGE_band' with 'GGE gel band' where source isolate does not contain 'gel'" VAR find_text = "GGE_band" repl_text = "GGE gel band" location = "anywhere" case_sensitive = true FOR EACH BioSource WHERE NOT CONTAINS("org.orgname.mod", "isolate", "gel") DO o = Resolve("org.orgname.mod") WHERE o.subtype = "isolate"; EditStringQual (o, "subname", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_164 "Edit isolate replace 'dgge gel band' (case insensitive) with 'DGGE gel band' where source isolate does not contain 'DGGE gel band' (case-sensitive)" VAR find_text = "dgge gel band" repl_text = "DGGE gel band" location = "anywhere" case_sensitive_action = false case_sensitive_constr = true FOR EACH BioSource WHERE NOT CONTAINS("org.orgname.mod", "isolate", repl_text, case_sensitive_constr) DO o = Resolve("org.orgname.mod") WHERE o.subtype = "isolate"; EditStringQual (o, "subname", find_text, repl_text, location, case_sensitive_action); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_165 "Edit isolate replace 'tgge gel band' (case insensitive) with 'TGGE gel band' where source isolate does not contain 'TGGE gel band' (case-sensitive)" VAR find_text = "tgge gel band" repl_text = "TGGE gel band" location = "anywhere" case_sensitive_action = false case_sensitive_constr = true FOR EACH BioSource WHERE NOT CONTAINS("org.orgname.mod", "isolate", repl_text, case_sensitive_constr) DO o = Resolve("org.orgname.mod") WHERE o.subtype = "isolate"; EditStringQual (o, "subname", find_text, repl_text, location, case_sensitive_action); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_166 "Edit isolate replace 'DGGE band' (case insensitive) with 'DGGE gel band'" VAR find_text = "DGGE band" repl_text = "DGGE gel band" location = "anywhere" case_sensitive = false FOR EACH BioSource DO o = Resolve("org.orgname.mod") WHERE o.subtype = "isolate"; EditStringQual (o, "subname", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_167 "Edit isolate replace 'TGGE band' (case insensitive) with 'TGGE gel band'" VAR find_text = "TGGE band" repl_text = "TGGE gel band" location = "anywhere" case_sensitive = false FOR EACH BioSource DO o = Resolve("org.orgname.mod") WHERE o.subtype = "isolate"; EditStringQual (o, "subname", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_168 "Edit isolate replace 'DGGE' (case insensitive) with 'DGGE gel band' where source isolate does not contain 'gel', allow 'gel' to be replaced by 'band' and 'gel band'" VAR find_text = "DGGE" repl_text = "DGGE gel band" location = "at the beginning" case_sensitive = false FOR EACH BioSource WHERE NOT CONTAINS("org.orgname.mod", "isolate", "gel", "synonyms.txt", "gel") DO o = Resolve("org.orgname.mod") WHERE o.subtype = "isolate"; EditStringQual (o, "subname", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_169 "Edit isolate replace 'TGGE' (case insensitive) with 'TGGE gel band' where source isolate does not contain 'gel band' (case-sensitive), allow 'gel band' to be replaced by 'gel' and 'band'" VAR find_text = "TGGE" repl_text = "TGGE gel band" location = "at the beginning" case_sensitive = false FOR EACH BioSource WHERE NOT CONTAINS("org.orgname.mod", "isolate", "gel", "synonyms.txt", "gel") DO o = Resolve("org.orgname.mod") WHERE o.subtype = "isolate"; EditStringQual (o, "subname", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_170 "Fix capitalization in common Mus musculus strains" FOR EACH BioSource DO o = Resolve("org.orgname.mod") WHERE o.subtype = "strain"; FixMouseStrains(o, "subname"); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_171 "Edit taxname replace ' sp' with ' sp.' where source dbxref does not start with 'taxon:'" VAR find_text = " sp" repl_text = " sp." location = "at the end" case_sensitive = true FOR EACH BioSource WHERE NOT STARTS("org.db.db", "taxon") DO EditStringQual ("org.taxname", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_172 "Edit taxname replace ' spp' with ' sp.' where source dbxref does not start with 'taxon:'" VAR find_text = " spp" repl_text = " sp." location = "at the end" case_sensitive = true FOR EACH BioSource WHERE NOT STARTS("org.db.db", "taxon") DO EditStringQual ("org.taxname", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_173 "Edit taxname replace ' spp.' with ' sp.' where source dbxref does not start with 'taxon:'" VAR find_text = " spp." repl_text = " sp." location = "at the end" case_sensitive = true FOR EACH BioSource WHERE NOT STARTS("org.db.db", "taxon") DO EditStringQual ("org.taxname", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_174 "Edit taxname replace ' sp ' with ' sp. ' where source dbxref does not start with 'taxon:' (case-sensitive)" VAR find_text = " sp " repl_text = " sp. " location = "anywhere" case_sensitive = true FOR EACH BioSource WHERE NOT STARTS("org.db.db", "taxon:", case_sensitive) DO EditStringQual ("org.taxname", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_175 "Edit host replace ' sp' with ' sp.'" VAR find_text = " sp" repl_text = " sp." location = "at the end" case_sensitive = true FOR EACH BioSource DO o = Resolve("org.orgname.mod") WHERE o.subtype = "nat-host"; EditStringQual (o, "subname", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_176 "Edit misc_feature note replace 'Intergenic spacer' (case insensitive) with 'intergenic spacer' where misc_feature note does not contain 'intergenic spacer' (case-sensitive)" VAR find_text = "Intergenic spacer" repl_text = "intergenic spacer" location = "anywhere" case_sensitive_edit = false case_sensitive_constr = true FOR EACH Misc_feat WHERE NOT CONTAINS("comment", repl_text, case_sensitive_constr) DO EditStringQual ("comment", find_text, repl_text, location, case_sensitive_edit); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_177 "Edit gene locus replace ' gene' (case insensitive) with '' where gene locus does not contain 'recombination' (ignore spaces), allow 'recombination' to be replaced by 'recombinatin', 'recombinaton', and 'recombonation' and where gene locus does not contain 'triple' (ignore spaces), allow 'triple' to be replaced by 'block'" VAR find_text = " gene" repl_text = "" location = "at the end" case_sensitive = false ignore_space = true FOR EACH Gene WHERE NOT CONTAINS("data.gene.locus", "recombination", case_sensitive, ignore_space, "synonyms.txt", "recombination") AND NOT CONTAINS("data.gene.locus", "triple", case_sensitive, ignore_space, "synonyms.txt", "triple") DO EditStringQual ("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_178 "Edit gene locus replace ' gene, partial cds' (case insensitive) with '' where gene locus does not contain 'recombination' (ignore spaces), allow 'recombination' to be replaced by 'recombinatin', 'recombinaton', and 'recombonation' and where gene locus does not contain 'triple' (ignore spaces), allow 'triple' to be replaced by 'block'" VAR find_text = " gene, partial cds" repl_text = "" location = "at the end" case_sensitive = false ignore_space = true FOR EACH Gene WHERE NOT CONTAINS("data.gene.locus", "recombination", case_sensitive, ignore_space, "synonyms.txt", "recombination") AND NOT CONTAINS("data.gene.locus", "triple", case_sensitive, ignore_space, "synonyms.txt", "triple") DO EditStringQual ("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_179 "Edit protein name replace ', partial CDS' (case insensitive) with ''" VAR find_text = ", partial CDS" repl_text = "" location = "at the end" case_sensitive = false FOR EACH Protein DO EditStringQual ("data.prot.name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_180 "Edit protein name replace '; partial CDS' (case insensitive) with ''" VAR find_text = "; partial CDS" repl_text = "" location = "at the end" case_sensitive = false FOR EACH Protein DO EditStringQual ("data.prot.name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_181 "Edit protein name replace 'partial CDS' (case insensitive) with ''" VAR find_text = "partial CDS" repl_text = "" location = "at the end" case_sensitive = false FOR EACH Protein DO EditStringQual ("data.prot.name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_182 "Edit protein name replace 'gene, partial CDS' (case insensitive) with '' where protein name does not contain 'recombination' (ignore spaces, ignore punctuation), allow 'recombination' to be replaced by 'recombinatin', 'recombinaton', and 'recombonation' and where protein name does not contain 'activating' (ignore spaces, ignore punctuation) and where protein name does not contain 'triple' (ignore spaces, ignore punctuation)" VAR find_text = "gene, partial CDS" repl_text = "" location = "at the end" case_sensitive = false ignore_space = true ignore_punctuation = true FOR EACH Protein DO o = Resolve("data.prot.name") WHERE NOT CONTAINS(o, "recombination", case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", "recombination") AND NOT CONTAINS(o, "activating", case_sensitive, ignore_space, ignore_punctuation) AND NOT CONTAINS(o, "triple", case_sensitive, ignore_space, ignore_punctuation); EditStringQual (o, "", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_183 "Edit protein name replace 'gene partial CDS' (case insensitive) with '' where protein name does not contain 'recombination' (ignore spaces, ignore punctuation), allow 'recombination' to be replaced by 'recombinatin', 'recombinaton', and 'recombonation' and where protein name does not contain 'activating' (ignore spaces, ignore punctuation) and where protein name does not contain 'triple' (ignore spaces, ignore punctuation)" VAR find_text = "gene partial CDS" repl_text = "" location = "at the end" case_sensitive = false ignore_space = true ignore_punctuation = true FOR EACH Protein DO o = Resolve("data.prot.name") WHERE NOT CONTAINS(o, "recombination", case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", "recombination") AND NOT CONTAINS(o, "activating", case_sensitive, ignore_space, ignore_punctuation) AND NOT CONTAINS(o, "triple", case_sensitive, ignore_space, ignore_punctuation); EditStringQual (o, "", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_184 "Edit protein name replace 'gene, partial protein' (case insensitive) with '' where protein name does not contain 'recombination' (ignore spaces, ignore punctuation), allow 'recombination' to be replaced by 'recombinatin', 'recombinaton', and 'recombonation' and where protein name does not contain 'activating' (ignore spaces, ignore punctuation) and where protein name does not contain 'triple' (ignore spaces, ignore punctuation)" VAR find_text = "gene, partial protein" repl_text = "" location = "at the end" case_sensitive = false ignore_space = true ignore_punctuation = true FOR EACH Protein DO o = Resolve("data.prot.name") WHERE NOT CONTAINS(o, "recombination", case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", "recombination") AND NOT CONTAINS(o, "activating", case_sensitive, ignore_space, ignore_punctuation) AND NOT CONTAINS(o, "triple", case_sensitive, ignore_space, ignore_punctuation); EditStringQual (o, "", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_185 "Edit protein name replace 'gene partial protein' (case insensitive) with '' where protein name does not contain 'recombination' (ignore spaces, ignore punctuation), allow 'recombination' to be replaced by 'recombinatin', 'recombinaton', and 'recombonation' and where protein name does not contain 'activating' (ignore spaces, ignore punctuation) and where protein name does not contain 'triple' (ignore spaces, ignore punctuation)" VAR find_text = "gene partial protein" repl_text = "" location = "at the end" case_sensitive = false ignore_space = true ignore_punctuation = true FOR EACH Protein DO o = Resolve("data.prot.name") WHERE NOT CONTAINS(o, "recombination", case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", "recombination") AND NOT CONTAINS(o, "activating", case_sensitive, ignore_space, ignore_punctuation) AND NOT CONTAINS(o, "triple", case_sensitive, ignore_space, ignore_punctuation); EditStringQual (o, "", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_186 "Edit protein name replace ', partial protein' (case insensitive) with ''" VAR find_text = ", partial protein" repl_text = "" location = "at the end" case_sensitive = false FOR EACH Protein DO EditStringQual ("data.prot.name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_187 "Edit protein name replace '; partial protein' (case insensitive) with ''" VAR find_text = "; partial protein" repl_text = "" location = "at the end" case_sensitive = false FOR EACH Protein DO EditStringQual ("data.prot.name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_188 "Edit protein name replace ' partial protein' (case insensitive) with ''" VAR find_text = " partial protein" repl_text = "" location = "at the end" case_sensitive = false FOR EACH Protein DO EditStringQual ("data.prot.name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_189 "Edit protein name replace ', partial' (case insensitive) with ''" VAR find_text = ", partial" repl_text = "" location = "at the end" case_sensitive = false FOR EACH Protein DO EditStringQual ("data.prot.name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_190 "Edit protein name replace '; partial' (case insensitive) with ''" VAR find_text = "; partial" repl_text = "" location = "at the end" case_sensitive = false FOR EACH Protein DO EditStringQual ("data.prot.name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_191 "Edit protein name replace ' partial' (case insensitive) with ''" VAR find_text = " partial" repl_text = "" location = "at the end" case_sensitive = false FOR EACH Protein DO EditStringQual ("data.prot.name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_192 "Edit protein name replace 'oxydase' (case insensitive) with 'oxidase'" VAR find_text = "oxydase" repl_text = "oxidase" location = "anywhere" case_sensitive = false FOR EACH Protein DO EditStringQual ("data.prot.name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_193 "Edit protein name replace 'oxigenase' (case insensitive) with 'oxygenase'" VAR find_text = "oxigenase" repl_text = "oxygenase" location = "anywhere" case_sensitive = false FOR EACH Protein DO EditStringQual ("data.prot.name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_194 "Edit protein name replace 'cytochorme' (case insensitive) with 'cytochrome'" VAR find_text = "cytochorme" repl_text = "cytochrome" location = "anywhere" case_sensitive = false FOR EACH Protein DO EditStringQual ("data.prot.name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_195 "Edit protein name replace 'citochrome' (case insensitive) with 'cytochrome'" VAR find_text = "citochrome" repl_text = "cytochrome" location = "anywhere" case_sensitive = false FOR EACH Protein DO EditStringQual ("data.prot.name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_196 "Edit protein name replace 'cytochome' (case insensitive) with 'cytochrome'" VAR find_text = "cytochome" repl_text = "cytochrome" location = "anywhere" case_sensitive = false FOR EACH Protein DO EditStringQual ("data.prot.name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_197 "Edit protein name replace 'cytochrom ' (case insensitive) with 'cytochrome '" VAR find_text = "cytochrom " repl_text = "cytochrome " location = "anywhere" case_sensitive = false FOR EACH Protein DO EditStringQual ("data.prot.name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_198 "Edit protein name replace 'polymeerase' (case insensitive) with 'polymerase'" VAR find_text = "polymeerase" repl_text = "polymerase" location = "anywhere" case_sensitive = false FOR EACH Protein DO EditStringQual ("data.prot.name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_199 "Edit protein name replace 'subunite ' (case insensitive) with 'subunit '" VAR find_text = "subunite" repl_text = "subunit " location = "anywhere" case_sensitive = false FOR EACH Protein DO EditStringQual ("data.prot.name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_200 "Edit rRNA product replace 'ribossomal' (case insensitive) with 'ribosomal'" VAR find_text = "ribossomal" repl_text = "ribosomal" location = "anywhere" case_sensitive = false FOR EACH rRNA DO EditStringQual ("data.rna.ext.name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_201 "Edit rRNA product replace 'ribosmal' (case insensitive) with 'ribosomal'" VAR find_text = "ribosmal" repl_text = "ribosomal" location = "anywhere" case_sensitive = false FOR EACH rRNA DO EditStringQual ("data.rna.ext.name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_202 "Edit rRNA product replace 'robosmal' (case insensitive) with 'ribosomal'" VAR find_text = "robosmal" repl_text = "ribosomal" location = "anywhere" case_sensitive = false FOR EACH rRNA DO EditStringQual ("data.rna.ext.name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_203 "Remove organism names from protein names" For each Protein Do FixProteinFormat("data.prot.name"); Done ------------------------------------------------------------------------------ MACRO Autofix_macro_204 "Apply cytochrome b to CDS product (overwrite existing text) where CDS product equals 'cytochrome b gene' (ignore spaces, ignore punctuation), allow 'gene' to be replaced by 'sequence', 'partial', 'complete', 'region', 'cytb', 'cyt b', 'partial sequence', 'complete sequence', '(cytb)', and '(cyt b)'" VAR new_value = "cytochrome b" existing_text = "eReplace" match = "cytochrome b gene" match1 = "gene" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH Protein DO o = Resolve("data.prot.name") WHERE EQUALS(o, match, case_sensitive, ignore_spaces, ignore_punctuation, "synonyms.txt", match, match1); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_205 "Apply cytb to gene locus (overwrite existing text) where gene locus equals 'cytochrome b (cytb)' (ignore spaces, ignore punctuation), allow 'cytochrome b (cytb)' to be replaced by 'cytochrome b (cytb) gene' and where protein name contains 'cytochrome b' (ignore spaces, ignore punctuation)" VAR new_value = "cyt b" existing_text = "eReplace" match = "cytochrome b (cytb)" match_prot = "cytochrome b" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH Gene WHERE EQUALS("data.gene.locus", match, case_sensitive, ignore_spaces, ignore_punctuation, "synonyms.txt", match) AND CONTAINS(PROTEIN_FOR_GENE("data.prot.name"), match_prot, case_sensitive, ignore_spaces, ignore_punctuation) DO SetStringQual ("data.gene.locus", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_206 "Apply cytochrome b to CDS product (overwrite existing text) where CDS product equals 'cytochrome b gene' (ignore spaces, ignore punctuation), allow 'gene' to be replaced by 'sequence', 'partial', 'complete', 'region', 'cytb', 'cyt b', 'partial sequence', 'complete sequence', '(cytb)', and '(cyt b)', allow 'cytochrome b gene' to be replaced by 'cytochrome b (cytb) gene' and where gene locus contains 'cytb'" VAR new_value = "cytochrome b" existing_text = "eReplace" match = "cytochrome b gene" match1 = "gene" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH Protein WHERE CONTAINS(GENE_FOR_PROTEIN("data.gene.locus"), "cytb") DO o = Resolve("data.prot.name") WHERE EQUALS(o, match, case_sensitive, ignore_spaces, ignore_punctuation, "synonyms.txt", match, match1); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_207 "Apply maturase K to CDS product (overwrite existing text) where CDS product equals 'maturase K gene' (ignore spaces, ignore punctuation), allow 'gene' to be replaced by 'partial', 'complete', 'region', 'sequence', 'matK', 'mat k', 'partial sequence', 'complete sequence', '(matK)', and '(mat K)'" VAR new_value = "maturase K" existing_text = "eReplace" match = "maturase K gene" match1 = "gene" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH Protein DO o = Resolve("data.prot.name") WHERE EQUALS(o, match, case_sensitive, ignore_spaces, ignore_punctuation, "synonyms.txt", match, match1); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_208 "Edit protein name replace 'cytochrome oxidase c subunit 1' (case insensitive) with 'cytochrome c oxidase subunit 1'" VAR find_text = "cytochrome oxidase c subunit 1" repl_text = "cytochrome c oxidase subunit 1" location = "anywhere" case_sensitive = false FOR EACH Protein DO EditStringQual ("data.prot.name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_209 "Edit protein name replace 'cytochrome oxidase c subunit I' (case insensitive) with 'cytochrome c oxidase subunit I'" VAR find_text = "cytochrome oxidase c subunit I" repl_text = "cytochrome c oxidase subunit 1" location = "anywhere" case_sensitive = false FOR EACH Protein DO EditStringQual ("data.prot.name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_210 "Edit protein name replace 'cytochrome c oxidae' (case insensitive) with 'cytochrome c oxidase'" VAR find_text = "cytochrome c oxidae" repl_text = "cytochrome c oxidase" location = "anywhere" case_sensitive = false FOR EACH Protein DO EditStringQual ("data.prot.name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_211 "Edit protein name replace 'cytochrome oxidae' (case insensitive) with 'cytochrome oxidase'" VAR find_text = "cytochrome oxidae" repl_text = "cytochrome oxidase" location = "anywhere" case_sensitive = false FOR EACH Protein DO EditStringQual ("data.prot.name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_212 "Edit protein name replace 'cytochrom c oxidase subunit 1' (case insensitive) with 'cytochrome c oxidase subunit 1'" VAR find_text = "cytochrom c oxidase subunit 1" repl_text = "cytochrome c oxidase subunit 1" location = "anywhere" case_sensitive = false FOR EACH Protein DO EditStringQual ("data.prot.name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_213 "Edit protein name replace 'cytochrom oxidase subunit 1' (case insensitive) with 'cytochrome oxidase subunit 1'" VAR find_text = "cytochrom oxidase subunit 1" repl_text = "cytochrome oxidase subunit 1" location = "anywhere" case_sensitive = false FOR EACH Protein DO EditStringQual ("data.prot.name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_217 "Edit protein name replace 'Cytochrome Oxidase unit ' (case insensitive) with 'cytochrome oxidase subunit ' where protein name does not contain 'subunit' (case-sensitive)" VAR find_text = "Cytochrome Oxidase unit " repl_text = "cytochrome oxidase subunit " location = "anywhere" case_sensitive_edit = false case_sensitive_constr = true FOR EACH Protein DO o = Resolve("data.prot.name") WHERE NOT CONTAINS(o, "subunit", case_sensitive_constr); EditStringQual (o, "", find_text, repl_text, location, case_sensitive_edit); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_218 "Edit protein name replace 'Cytochrome c Oxidase unit ' (case insensitive) with 'cytochrome c oxidase subunit ' where protein name does not contain 'subunit' (case-sensitive)" VAR find_text = "Cytochrome c Oxidase unit " repl_text = "cytochrome c oxidase subunit " location = "anywhere" case_sensitive_edit = false case_sensitive_constr = true FOR EACH Protein DO o = Resolve("data.prot.name") WHERE NOT CONTAINS(o, "subunit", case_sensitive_constr); EditStringQual (o, "", find_text, repl_text, location, case_sensitive_edit); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_219 "Apply cytochrome c oxidase subunit I to CDS product (overwrite existing text) where CDS product equals 'cytochrome c oxidase subunit I gene' (ignore spaces, ignore punctuation), allow 'oxidase' to be replaced by 'oxydase', allow 'gene' to be replaced by 'sequence', 'partial', 'complete', 'partial sequence', 'complete sequence', 'region', and 'protein', allow 'cytochrome c oxidase subunit I gene' to be replaced by 'cytochrome c oxidase I', 'cytochrome c oxidase I gene', 'cytochrome c subunit I', and 'cytochrome c oxidase subunit I gene protein', allow 'I' to be replaced by 'one', allow 'oxidase subunit' to be replaced by 'subunit'" VAR new_value = "cytochrome c oxidase subunit I" existing_text = "eReplace" match = "cytochrome c oxidase subunit I gene" match1 = "oxidase" match2 = "gene" match3 = "I" match4 = "oxidase subunit" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH Protein DO o = Resolve("data.prot.name") WHERE EQUALS(o, match, case_sensitive, ignore_spaces, ignore_punctuation, "synonyms.txt", match, match1, match2, match3, match4); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_220 "Apply cytochrome c oxidase subunit II to CDS product (overwrite existing text) where CDS product equals 'cytochrome c oxidase subunit II gene' (ignore spaces, ignore punctuation), allow 'oxidase' to be replaced by 'oxydase', allow 'gene' to be replaced by 'sequence', 'partial', 'complete', 'partial sequence', 'complete sequence', 'region', and 'protein', allow 'cytochrome c oxidase subunit II gene' to be replaced by 'cytochrome c oxidase II gene', 'cytochrome c oxidase II', 'cytochrome c subunit II', and 'cytochrome c oxidase subunit II protein', allow 'II' to be replaced by 'two', allow 'oxidase subunit' to be replaced by 'subunit'" VAR new_value = "cytochrome c oxidase subunit II" existing_text = "eReplace" match = "cytochrome c oxidase subunit II gene" match1 = "oxidase" match2 = "gene" match3 = "II" match4 = "oxidase subunit" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH Protein DO o = Resolve("data.prot.name") WHERE EQUALS(o, match, case_sensitive, ignore_spaces, ignore_punctuation, "synonyms.txt", match, match1, match2, match3, match4); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_221 "Apply cytochrome oxidase subunit I to CDS product (overwrite existing text) where CDS product equals 'cytochrome oxidase subunit I gene' (ignore spaces, ignore punctuation), allow 'oxidase' to be replaced by 'oxydase', allow 'gene' to be replaced by 'sequence', 'partial', 'complete', 'partial sequence', 'complete sequence', 'region', and 'protein', allow 'cytochrome oxidase subunit I gene' to be replaced by 'cytochrome oxidase I gene', 'cytochrome oxidase I', and 'cytochrome subunit I', allow 'I' to be replaced by 'one', allow ' I' to be replaced by ' i', allow 'oxidase subunit' to be replaced by 'subunit'" VAR new_value = "cytochrome oxidase subunit I" existing_text = "eReplace" match = "cytochrome oxidase subunit I gene" match1 = "oxidase" match2 = "gene" match3 = "I" match4 = "oxidase subunit" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH Protein DO o = Resolve("data.prot.name") WHERE EQUALS(o, match, case_sensitive, ignore_spaces, ignore_punctuation, "synonyms.txt", match, match1, match2, match3, match4); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_222 "Apply cytochrome oxidase subunit II to CDS product (overwrite existing text) where CDS product equals 'cytochrome oxidase subunit II gene' (ignore spaces, ignore punctuation), allow 'oxidase' to be replaced by 'oxydase', allow 'gene' to be replaced by 'sequence', 'partial', 'complete', 'partial sequence', 'complete sequence', 'region', and 'protein', allow 'cytochrome oxidase subunit II gene' to be replaced by 'cytochrome oxidase II gene', 'cytochrome oxidase II', and 'cytochrome subunit II', allow 'II' to be replaced by 'two', allow 'II' to be replaced by 'ii', allow 'oxidase subunit' to be replaced by 'subunit'" VAR new_value = "cytochrome oxidase subunit II" existing_text = "eReplace" match = "cytochrome oxidase subunit II gene" match1 = "oxidase" match2 = "gene" match3 = "II" match4 = "oxidase subunit" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH Protein DO o = Resolve("data.prot.name") WHERE EQUALS(o, match, case_sensitive, ignore_spaces, ignore_punctuation, "synonyms.txt", match, match1, match2, match3, match4); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_223 "Apply cytochrome oxidase subunit III to CDS product (overwrite existing text) where CDS product equals 'cytochrome oxidase subunit III gene' (ignore spaces, ignore punctuation), allow 'oxidase' to be replaced by 'oxydase', allow 'gene' to be replaced by 'sequence', 'partial', 'complete', 'partial sequence', 'complete sequence', 'region', and 'protein', allow 'cytochrome oxidase subunit III gene' to be replaced by 'cytochrome oxidase III gene', 'cytochrome oxidase III', and 'cytochrome subunit III', allow 'III' to be replaced by 'three' and 'iii', allow 'oxidase subunit' to be replaced by 'subunit'" VAR new_value = "cytochrome oxidase subunit III" existing_text = "eReplace" match = "cytochrome oxidase subunit III gene" match1 = "oxidase" match2 = "gene" match3 = "III" match4 = "oxidase subunit" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH Protein DO o = Resolve("data.prot.name") WHERE EQUALS(o, match, case_sensitive, ignore_spaces, ignore_punctuation, "synonyms.txt", match, match1, match2, match3, match4); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_224 "Apply cytochrome c oxidase subunit 1 to CDS product (overwrite existing text) where CDS product equals 'cytochrome c oxidase subunit 1 gene' (ignore spaces, ignore punctuation), allow 'oxidase' to be replaced by 'oxydase', allow 'gene' to be replaced by 'sequence', 'partial', 'complete', 'partial sequence', 'complete sequence', 'region', and 'protein', allow 'cytochrome c oxidase subunit 1 gene' to be replaced by 'cytochrome c oxidase 1 gene', 'cytochrome c oxidase 1', and 'cytochrome c subunit 1', allow '1' to be replaced by 'one', allow 'oxidase subunit' to be replaced by 'subunit'" VAR new_value = "cytochrome c oxidase subunit 1" existing_text = "eReplace" match = "cytochrome c oxidase subunit 1 gene" match1 = "oxidase" match2 = "gene" match3 = "1" match4 = "oxidase subunit" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH Protein DO o = Resolve("data.prot.name") WHERE EQUALS(o, match, case_sensitive, ignore_spaces, ignore_punctuation, "synonyms.txt", match, match1, match2, match3, match4); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_225 "Apply cytochrome oxidase subunit 1 to CDS product (overwrite existing text) where CDS product equals 'cytochrome oxidase subunit 1 gene' (ignore spaces, ignore punctuation), allow 'oxidase' to be replaced by 'oxydase', allow 'gene' to be replaced by 'sequence', 'partial', 'complete', 'partial sequence', 'complete sequence', 'region', and 'protein', allow 'cytochrome oxidase subunit 1 gene' to be replaced by 'cytochrome oxidase 1', 'cytochrome oxidase 1 gene', and 'cytochrome subunit 1', allow '1' to be replaced by 'one', allow 'oxidase subunit' to be replaced by 'subunit'" VAR new_value = "cytochrome oxidase subunit 1" existing_text = "eReplace" match = "cytochrome oxidase subunit 1 gene" match1 = "oxidase" match2 = "gene" match3 = "1" match4 = "oxidase subunit" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH Protein DO o = Resolve("data.prot.name") WHERE EQUALS(o, match, case_sensitive, ignore_spaces, ignore_punctuation, "synonyms.txt", match, match1, match2, match3, match4); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_226 "Apply COI to gene locus (overwrite existing text) where gene locus equals 'cytochrome oxidase subunit I (COI)' (case-sensitive, ignore spaces, ignore punctuation) and where protein name equals 'cytochrome oxidase subunit I (COI)', allow 'cytochrome oxidase subunit I (COI)' to be replaced by 'cytochrome oxidase subunit I'" VAR new_value = "COI" existing_text = "eReplace" match = "cytochrome oxidase subunit I (COI)" case_sensitive = true ignore_spaces = true ignore_punctuation = true FOR EACH Gene WHERE EQUALS("data.gene.locus", match, case_sensitive, ignore_spaces, ignore_punctuation) AND EQUALS(PROTEIN_FOR_GENE("data.prot.name"), match, "synonyms.txt", match) DO SetStringQual ("data.gene.locus", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_227 "Apply COI to gene locus (overwrite existing text) where gene locus equals 'cytochrome oxidase I (COI)' (case-sensitive, ignore spaces, ignore punctuation) and where protein name equals 'cytochrome oxidase I (COI)', allow 'cytochrome oxidase I (COI)' to be replaced by 'cytochrome oxidase subunit I (COI)'" VAR new_value = "COI" existing_text = "eReplace" match = "cytochrome oxidase I (COI)" case_sensitive = true ignore_spaces = true ignore_punctuation = true FOR EACH Gene WHERE EQUALS("data.gene.locus", match, case_sensitive, ignore_spaces, ignore_punctuation) AND EQUALS(PROTEIN_FOR_GENE("data.prot.name"), match, "synonyms.txt", match) DO SetStringQual ("data.gene.locus", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_228 "Apply cytochrome oxidase subunit I to protein name (overwrite existing text) where gene locus contains 'COI' (case-sensitive) and where protein name equals 'cytochrome oxidase I (COI)', allow 'cytochrome oxidase I (COI)' to be replaced by 'cytochrome oxidase subunit I (COI)'" VAR new_value = "cytochrome oxidase subunit I" existing_text = "eReplace" case_sensitive = true match = "cytochrome oxidase I (COI)" FOR EACH Protein WHERE CONTAINS(GENE_FOR_PROTEIN("data.gene.locus"), "COI", case_sensitive) DO o = Resolve("data.prot.name") WHERE EQUALS(o, match, "synonyms.txt", match); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_229 "Apply cytochrome oxidase subunit I to protein name (overwrite existing text) where gene locus contains 'COI' (case-sensitive) and where protein name equals 'cytochrome oxidase I (COI)'" VAR new_value = "cytochrome oxidase subunit I" existing_text = "eReplace" case_sensitive = true match = "cytochrome oxidase I (COI)" FOR EACH Protein WHERE CONTAINS(GENE_FOR_PROTEIN("data.gene.locus"), "COI", case_sensitive) DO o = Resolve("data.prot.name") WHERE EQUALS(o, match); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_230 "Apply cytochrome oxidase subunit III to protein name (overwrite existing text) where gene locus contains 'COIII' (case-sensitive) and where protein name equals 'cytochrome oxidase subunit III (COIII) gene' (ignore spaces, ignore punctuation), allow 'cytochrome oxidase subunit III (COIII) gene' to be replaced by 'cytochrome oxidase subunit 3 (COIII) gene', 'cytochrome oxidase subunit 3 (COIII)', and 'cytochrome oxidase subunit III (COIII)'" VAR new_value = "cytochrome oxidase subunit III" existing_text = "eReplace" case_sensitive_constr1 = true VAR match = "cytochrome oxidase subunit III (COIII) gene" case_sensitive_constr2 = false ignore_space = true ignore_punctuation = true FOR EACH Protein WHERE CONTAINS(GENE_FOR_PROTEIN("data.gene.locus"), "COIII", case_sensitive_constr1) DO o = Resolve("data.prot.name") WHERE EQUALS(o, match, case_sensitive_constr2, ignore_space, ignore_punctuation, "synonyms.txt", match); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_231 "Edit gene locus replace 'mtDNA COI' with 'COI' where gene locus equals 'mtDNA COI' (case-sensitive)" VAR find_text = "mtDNA COI" repl_text = "COI" location = "anywhere" case_sensitive = true FOR EACH Gene WHERE EQUALS("data.gene.locus", find_text, case_sensitive) DO EditStringQual ("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_232 "Apply cytochrome c oxidase subunit 2 to CDS product (overwrite existing text) where CDS product equals 'cytochrome c oxidase subunit 2 gene' (ignore spaces, ignore punctuation), allow 'oxidase' to be replaced by 'oxydase', allow 'gene' to be replaced by 'partial', 'complete', 'sequence', 'region', 'partial sequence', 'complete sequence', and 'protein', allow 'cytochrome c oxidase subunit 2 gene' to be replaced by 'cytochrome c oxidase 2 gene', 'cytochrome c oxidase 2', and 'cytochrome c subunit 2', allow '2' to be replaced by 'two', allow 'oxidase subunit' to be replaced by 'subunit'" VAR new_value = "cytochrome c oxidase subunit 2" existing_text = "eReplace" match = "cytochrome c oxidase subunit 2 gene" match1 = "oxidase" match2 = "gene" match3 = "2" match4 = "oxidase subunit" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH Protein DO o = Resolve("data.prot.name") WHERE EQUALS(o, match, case_sensitive, ignore_spaces, ignore_punctuation, "synonyms.txt", match, match1, match2, match3, match4); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_233 "Apply cytochrome oxidase subunit 2 to CDS product (overwrite existing text) where CDS product equals 'cytochrome oxidase subunit 2 gene' (ignore spaces, ignore punctuation), allow 'oxidase' to be replaced by 'oxydase', allow 'gene' to be replaced by 'partial', 'complete', 'sequence', 'region', 'partial sequence', 'complete sequence', and 'protein', allow 'cytochrome oxidase subunit 2 gene' to be replaced by 'cytochrome oxidase 2 gene', 'cytochrome oxidase 2', and 'cytochrome subunit 2', allow '2' to be replaced by 'two', allow 'oxidase subunit' to be replaced by 'subunit'" VAR new_value = "cytochrome oxidase subunit 2" existing_text = "eReplace" match = "cytochrome oxidase subunit 2 gene" match1 = "oxidase" match2 = "gene" match3 = "2" match4 = "oxidase subunit" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH Protein DO o = Resolve("data.prot.name") WHERE EQUALS(o, match, case_sensitive, ignore_spaces, ignore_punctuation, "synonyms.txt", match, match1, match2, match3, match4); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_234 "Apply cytochrome oxidase subunit 3 to CDS product (overwrite existing text) where CDS product equals 'cytochrome oxidase subunit 3 gene' (ignore spaces, ignore punctuation), allow 'oxidase' to be replaced by 'oxydase', allow 'gene' to be replaced by 'partial', 'complete', 'sequence', 'region', 'partial sequence', 'complete sequence', and 'protein', allow 'cytochrome oxidase subunit 3 gene' to be replaced by 'cytochrome oxidase 3 gene', 'cytochrome oxidase 3', and 'cytochrome subunit 3', allow '3' to be replaced by 'three', allow 'oxidase subunit' to be replaced by 'subunit'" VAR new_value = "cytochrome oxidase subunit 3" existing_text = "eReplace" match = "cytochrome oxidase subunit 3 gene" match1 = "oxidase" match2 = "gene" match3 = "3" match4 = "oxidase subunit" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH Protein DO o = Resolve("data.prot.name") WHERE EQUALS(o, match, case_sensitive, ignore_spaces, ignore_punctuation, "synonyms.txt", match, match1, match2, match3, match4); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_235 "Apply ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit to CDS product (overwrite existing text) where CDS product equals 'ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit gene' (ignore spaces, ignore punctuation), allow 'gene' to be replaced by 'complete sequence', 'region', 'complete', 'partial', 'sequence', 'rbcL', 'partial sequence', 'protein', and 'subunit', allow 'large subunit gene' to be replaced by 'lsu' and 'large'" VAR new_value = "ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit" existing_text = "eReplace" match = "ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit gene" match1 = "gene" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH Protein DO o = Resolve("data.prot.name") WHERE EQUALS(o, match, case_sensitive, ignore_spaces, ignore_punctuation, "synonyms.txt", match, match1); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_236 "Apply ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit to CDS product (overwrite existing text) where CDS product equals 'ribulose-1,5-bisphosphate carboxylase/oxygenase gene' (ignore spaces, ignore punctuation), allow 'gene' to be replaced by 'complete sequence', 'region', 'complete', 'partial', 'sequence', 'rbcL', 'partial sequence', 'protein', and 'subunit', allow 'ribulose-1,5-bisphosphate carboxylase/oxygenase gene' to be replaced by 'ribulose-1,5-bisphosphate carboxylase/oxygenase' and 'ribulose 1,5-bisphosphate carboxylase oxygenase' and where gene locus equals 'rbcl gene' (ignore spaces, ignore punctuation), allow 'rbcl gene' to be replaced by 'rbcl', allow 'gene' to be replaced by 'sequence', 'protein', 'partial sequence', 'partial protein', and 'partial gene'" VAR new_value = "ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit" existing_text = "eReplace" match = "ribulose-1,5-bisphosphate carboxylase/oxygenase gene" match1 = "gene" case_sensitive = false ignore_spaces = true ignore_punctuation = true VAR match_gene = "rbcl gene" FOR EACH Protein WHERE EQUALS(GENE_FOR_PROTEIN("data.gene.locus"), match_gene, case_sensitive, ignore_spaces, ignore_punctuation, "synonyms.txt", match_gene) DO o = Resolve("data.prot.name") WHERE EQUALS(o, match, case_sensitive, ignore_spaces, ignore_punctuation, "synonyms.txt", match, match1); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_237 "Apply ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit to CDS product (overwrite existing text) where CDS product equals 'ribulose-1,5-bisphosphate carboxylase/oxygenase gene' (ignore spaces, ignore punctuation), allow 'gene' to be replaced by 'complete sequence', 'region', 'complete', 'partial', 'sequence', 'rbcS', 'partial sequence', 'protein', and 'subunit', allow 'ribulose-1,5-bisphosphate carboxylase/oxygenase gene' to be replaced by 'ribulose-1,5-bisphosphate carboxylase/oxygenase' and 'ribulose 1,5-bisphosphate carboxylase oxygenase' and where gene locus equals 'rbcs gene' (ignore spaces, ignore punctuation), allow 'rbcs gene' to be replaced by 'rbcs', allow 'gene' to be replaced by 'sequence', 'protein', 'partial gene', 'partial sequence', and 'partial protein'" VAR new_value = "ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit" existing_text = "eReplace" match = "ribulose-1,5-bisphosphate carboxylase/oxygenase gene" match1 = "gene" case_sensitive = false ignore_spaces = true ignore_punctuation = true VAR match_gene = "rbcs gene" FOR EACH Protein WHERE EQUALS(GENE_FOR_PROTEIN("data.gene.locus"), match_gene, case_sensitive, ignore_spaces, ignore_punctuation, "synonyms.txt", match_gene) DO o = Resolve("data.prot.name") WHERE EQUALS(o, match, case_sensitive, ignore_spaces, ignore_punctuation, "synonyms.txt", match, match1); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_238 "Apply ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit to CDS product (overwrite existing text) where CDS product equals 'ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit gene' (ignore spaces, ignore punctuation), allow 'gene' to be replaced by 'partial', 'complete', 'partial sequence', 'region', 'sequence', 'rbcS', 'complete sequence', and 'protein'" VAR new_value = "ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit" existing_text = "eReplace" match = "ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit gene" match1 = "gene" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH Protein DO o = Resolve("data.prot.name") WHERE EQUALS(o, match, case_sensitive, ignore_spaces, ignore_punctuation, "synonyms.txt", match, match1); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_239 "Apply MHC class I antigen to protein name (overwrite existing text) where object text equals 'MHC CLASS I ANTIGEN gene' (ignore spaces, ignore punctuation), allow 'gene' to be replaced by 'sequence', 'partial sequence', 'complete sequence', 'partial', 'complete', and 'protein'" VAR new_value = "MHC class I antigen" existing_text = "eReplace" match = "MHC CLASS I ANTIGEN gene" match1 = "gene" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH Protein DO o = Resolve("data.prot.name") WHERE EQUALS(o, match, case_sensitive, ignore_spaces, ignore_punctuation, "synonyms.txt", match, match1); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_240 "Apply MHC class I antigen to mRNA product (overwrite existing text) where object text equals 'MHC CLASS I ANTIGEN gene' (ignore spaces, ignore punctuation), allow 'gene' to be replaced by 'sequence', 'partial sequence', 'complete sequence', 'partial', 'complete', and 'protein'" VAR new_value = "MHC class I antigen" existing_text = "eReplace" match = "MHC CLASS I ANTIGEN gene" match1 = "gene" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH mRNA WHERE EQUALS("data.rna.ext.name", match, case_sensitive, ignore_spaces, ignore_punctuation, "synonyms.txt", match, match1) DO SetStringQual ("data.rna.ext.name", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_241 "Apply MHC class II antigen to protein name (overwrite existing text) where object text equals 'MHC CLASS II ANTIGEN gene' (ignore spaces, ignore punctuation), allow 'gene' to be replaced by 'sequence', 'partial sequence', 'complete sequence', 'partial', 'complete', and 'protein'" VAR new_value = "MHC class II antigen" existing_text = "eReplace" match = "MHC CLASS II ANTIGEN gene" match1 = "gene" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH Protein DO o = Resolve("data.prot.name") WHERE EQUALS(o, match, case_sensitive, ignore_spaces, ignore_punctuation, "synonyms.txt", match, match1); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_242 "Apply MHC class II antigen to mRNA product (overwrite existing text) where object text equals 'MHC CLASS II ANTIGEN gene' (ignore spaces, ignore punctuation), allow 'gene' to be replaced by 'sequence', 'partial sequence', 'complete sequence', 'partial', 'complete', and 'protein'" VAR new_value = "MHC class II antigen" existing_text = "eReplace" match = "MHC CLASS II ANTIGEN gene" match1 = "gene" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH mRNA WHERE EQUALS("data.rna.ext.name", match, case_sensitive, ignore_spaces, ignore_punctuation, "synonyms.txt", match, match1) DO SetStringQual ("data.rna.ext.name", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_243 "Apply ND1 to gene locus (overwrite existing text) where gene locus equals 'NADH dehydrogenase subunit 1 gene (ND1)' (ignore spaces, ignore punctuation), allow 'gene' to be replaced by 'sequence', 'partial sequence', 'complete sequence', 'mitochondrial sequence', and 'mtDNA' and where protein name contains 'NADH dehydrogenase subunit 1' (ignore spaces, ignore punctuation)" VAR new_value = "ND1" existing_text = "eReplace" match = "NADH dehydrogenase subunit 1 gene (ND1)" prot = "NADH dehydrogenase subunit 1" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH Gene WHERE EQUALS("data.gene.locus", match, case_sensitive, ignore_spaces, ignore_punctuation, "synonyms.txt", match) AND CONTAINS(PROTEIN_FOR_GENE("data.prot.name"), prot, case_sensitive, ignore_spaces, ignore_punctuation) DO SetStringQual ("data.gene.locus", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_244 "Edit protein name replace 'NADH dehydrogenase subunit 1 (ND1)' (case insensitive) with 'NADH dehydrogenase subunit 1' where gene locus equals 'ND1' (ignore spaces, ignore punctuation) and where protein name equals 'NADH dehydrogenase subunit 1 (ND1)' (ignore spaces, ignore punctuation), allow 'NADH dehydrogenase subunit 1 (ND1)' to be replaced by 'NADH dehydrogenase subunit 1 (ND1) gene', 'NADH dehydrogenase subunit 1 (ND1) sequence', 'NADH dehydrogenase subunit 1 (ND1) partial sequence', and 'NADH dehydrogenase subunit 1 (ND1) partial protein'" VAR find_text = "NADH dehydrogenase subunit 1 (ND1)" repl_text = "NADH dehydrogenase subunit 1" location = "anywhere" case_sensitive = false ignore_space = true ignore_punctuation = true FOR EACH Protein WHERE EQUALS(GENE_FOR_PROTEIN("data.gene.locus"), "ND1", case_sensitive, ignore_space, ignore_punctuation) DO o = Resolve("data.prot.name") WHERE EQUALS(o, find_text, case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", find_text); EditStringQual (o, "", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_245 "Apply ND2 to gene locus (overwrite existing text) where gene locus equals 'NADH dehydrogenase subunit 2 gene (ND2)' (ignore spaces, ignore punctuation), allow 'gene' to be replaced by 'sequence', 'partial sequence', 'complete sequence', 'mitochondrial sequence', and 'mtDNA' and where protein name contains 'NADH dehydrogenase subunit 2' (ignore spaces, ignore punctuation)" VAR new_value = "ND2" existing_text = "eReplace" match = "NADH dehydrogenase subunit 2 gene (ND2)" prot = "NADH dehydrogenase subunit 2" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH Gene WHERE EQUALS("data.gene.locus", match, case_sensitive, ignore_spaces, ignore_punctuation, "synonyms.txt", match) AND CONTAINS(PROTEIN_FOR_GENE("data.prot.name"), prot, case_sensitive, ignore_spaces, ignore_punctuation) DO SetStringQual ("data.gene.locus", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_246 "Edit protein name replace 'NADH dehydrogenase subunit 2 (ND2)' (case insensitive) with 'NADH dehydrogenase subunit 2' where gene locus equals 'ND2' (ignore spaces, ignore punctuation)" VAR find_text = "NADH dehydrogenase subunit 2 (ND2)" repl_text = "NADH dehydrogenase subunit 2" location = "anywhere" case_sensitive = false ignore_space = true ignore_punctuation = true FOR EACH Protein WHERE EQUALS(GENE_FOR_PROTEIN("data.gene.locus"), "ND2", case_sensitive, ignore_space, ignore_punctuation) DO o = Resolve("data.prot.name"); EditStringQual (o, "", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_247 "Apply ND3 to gene locus (overwrite existing text) where gene locus equals 'NADH dehydrogenase subunit 3 gene (ND3)' (ignore spaces, ignore punctuation), allow 'gene' to be replaced by 'sequence', 'partial sequence', 'complete sequence', 'mitochondrial sequence', and 'mtDNA' and where protein name contains 'NADH dehydrogenase subunit 3' (ignore spaces, ignore punctuation)" VAR new_value = "ND3" existing_text = "eReplace" match = "NADH dehydrogenase subunit 3 gene (ND3)" prot = "NADH dehydrogenase subunit 3" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH Gene WHERE EQUALS("data.gene.locus", match, case_sensitive, ignore_spaces, ignore_punctuation, "synonyms.txt", match) AND CONTAINS(PROTEIN_FOR_GENE("data.prot.name"), prot, case_sensitive, ignore_spaces, ignore_punctuation) DO SetStringQual ("data.gene.locus", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_248 "Edit protein name replace 'NADH dehydrogenase subunit 3 (ND3)' (case insensitive) with 'NADH dehydrogenase subunit 3' where gene locus equals 'ND3' (ignore spaces, ignore punctuation)" VAR find_text = "NADH dehydrogenase subunit 3 (ND3)" repl_text = "NADH dehydrogenase subunit 3" location = "anywhere" case_sensitive = false ignore_space = true ignore_punctuation = true FOR EACH Protein WHERE EQUALS(GENE_FOR_PROTEIN("data.gene.locus"), "ND3", case_sensitive, ignore_space, ignore_punctuation) DO o = Resolve("data.prot.name"); EditStringQual (o, "", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_249 "Apply ND4 to gene locus (overwrite existing text) where gene locus equals 'NADH dehydrogenase subunit 4 gene (ND4)' (ignore spaces, ignore punctuation), allow 'gene' to be replaced by 'sequence', 'partial sequence', 'complete sequence', 'mitochondrial sequence', and 'mtDNA' and where protein name contains 'NADH dehydrogenase subunit 4' (ignore spaces, ignore punctuation)" VAR new_value = "ND4" existing_text = "eReplace" match = "NADH dehydrogenase subunit 4 gene (ND4)" prot = "NADH dehydrogenase subunit 4" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH Gene WHERE EQUALS("data.gene.locus", match, case_sensitive, ignore_spaces, ignore_punctuation, "synonyms.txt", match) AND CONTAINS(PROTEIN_FOR_GENE("data.prot.name"), prot, case_sensitive, ignore_spaces, ignore_punctuation) DO SetStringQual ("data.gene.locus", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_250 "Edit protein name replace 'NADH dehydrogenase subunit 4 (ND4)' (case insensitive) with 'NADH dehydrogenase subunit 4' where gene locus equals 'ND4' (ignore spaces, ignore punctuation)" VAR find_text = "NADH dehydrogenase subunit 4 (ND4)" repl_text = "NADH dehydrogenase subunit 4" location = "anywhere" case_sensitive = false ignore_space = true ignore_punctuation = true FOR EACH Protein WHERE EQUALS(GENE_FOR_PROTEIN("data.gene.locus"), "ND4", case_sensitive, ignore_space, ignore_punctuation) DO o = Resolve("data.prot.name"); EditStringQual (o, "", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_251 "Apply ND5 to gene locus (overwrite existing text) where gene locus equals 'NADH dehydrogenase subunit 5 gene (ND5)' (ignore spaces, ignore punctuation), allow 'gene' to be replaced by 'sequence', 'partial sequence', 'complete sequence', 'mitochondrial sequence', and 'mtDNA' and where protein name contains 'NADH dehydrogenase subunit 5' (ignore spaces, ignore punctuation)" VAR new_value = "ND5" existing_text = "eReplace" match = "NADH dehydrogenase subunit 5 gene (ND5)" prot = "NADH dehydrogenase subunit 5" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH Gene WHERE EQUALS("data.gene.locus", match, case_sensitive, ignore_spaces, ignore_punctuation, "synonyms.txt", match) AND CONTAINS(PROTEIN_FOR_GENE("data.prot.name"), prot, case_sensitive, ignore_spaces, ignore_punctuation) DO SetStringQual ("data.gene.locus", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_252 "Edit protein name replace 'NADH dehydrogenase subunit 5 (ND5)' (case insensitive) with 'NADH dehydrogenase subunit 5' where gene locus equals 'ND5' (ignore spaces, ignore punctuation)" VAR find_text = "NADH dehydrogenase subunit 5 (ND5)" repl_text = "NADH dehydrogenase subunit 5" location = "anywhere" case_sensitive = false ignore_space = true ignore_punctuation = true FOR EACH Protein WHERE EQUALS(GENE_FOR_PROTEIN("data.gene.locus"), "ND5", case_sensitive, ignore_space, ignore_punctuation) DO o = Resolve("data.prot.name"); EditStringQual (o, "", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_253 "Apply ND6 to gene locus (overwrite existing text) where gene locus equals 'NADH dehydrogenase subunit 6 gene (ND6)' (ignore spaces, ignore punctuation), allow 'gene' to be replaced by 'sequence', 'partial sequence', 'complete sequence', 'mitochondrial sequence', and 'mtDNA' and where protein name contains 'NADH dehydrogenase subunit 6' (ignore spaces, ignore punctuation)" VAR new_value = "ND6" existing_text = "eReplace" match = "NADH dehydrogenase subunit 6 gene (ND6)" prot = "NADH dehydrogenase subunit 6" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH Gene WHERE EQUALS("data.gene.locus", match, case_sensitive, ignore_spaces, ignore_punctuation, "synonyms.txt", match) AND CONTAINS(PROTEIN_FOR_GENE("data.prot.name"), prot, case_sensitive, ignore_spaces, ignore_punctuation) DO SetStringQual ("data.gene.locus", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_254 "Edit gene locus replace 'NADH dehydrogenase subunit 6 (ND6)' (case insensitive) with 'ND6' where protein name equals 'NADH dehydrogenase subunit 6 (ND6)' (ignore spaces, ignore punctuation)" VAR find_text = "NADH dehydrogenase subunit 6 (ND6)" repl_text = "ND6" location = "anywhere" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH Gene WHERE EQUALS(PROTEIN_FOR_GENE("data.prot.name"), find_text, case_sensitive, ignore_spaces, ignore_punctuation) DO EditStringQual ("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_255 "Edit protein name replace 'NADH dehydrogenase subunit 6 (ND6)' (case insensitive) with 'NADH dehydrogenase subunit 6' where gene locus equals 'ND6' (ignore spaces, ignore punctuation)" VAR find_text = "NADH dehydrogenase subunit 6 (ND6)" repl_text = "NADH dehydrogenase subunit 6" location = "anywhere" case_sensitive = false ignore_space = true ignore_punctuation = true FOR EACH Protein WHERE EQUALS(GENE_FOR_PROTEIN("data.gene.locus"), "ND6", case_sensitive, ignore_space, ignore_punctuation) DO o = Resolve("data.prot.name"); EditStringQual (o, "", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_256 "Apply NADH dehydrogenase subunit 1 to protein name (overwrite existing text) where object text equals 'NADH dehydrogenase subunit 1 gene' (ignore spaces, ignore punctuation), allow 'gene' to be replaced by 'sequence', 'partial sequence', 'complete sequence', 'partial', 'complete', 'gene sequence', and 'protein', allow 'NADH dehydrogenase subunit 1 gene' to be replaced by 'NADH dehydrogenase 1 gene' and 'NADH dehydrogenase 1', allow '1' to be replaced by 'one'" VAR new_value = "NADH dehydrogenase subunit 1" match1 = "NADH dehydrogenase subunit 1 gene" match2 = "gene" match3 = "1" existing_text = "eReplace" case_sensitive = false ignore_space = true ignore_punctuation = true FOR EACH Protein WHERE EQUALS("data.prot.name", match1, case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", match1, match2, match3) DO obj = Resolve("data.prot.name") WHERE EQUALS(obj, match1, case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", match1, match2, match3); SetStringQual (obj, "", new_value, existing_text); UpdatemRNAProduct(); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_257 "Apply NADH dehydrogenase subunit 2 to protein name (overwrite existing text) where object text equals 'NADH dehydrogenase subunit 2 gene' (ignore spaces, ignore punctuation), allow 'gene' to be replaced by 'sequence', 'partial sequence', 'complete sequence', 'partial', 'complete', 'gene sequence', and 'protein', allow 'NADH dehydrogenase subunit 2 gene' to be replaced by 'NADH dehydrogenase 2 gene' and 'NADH dehydrogenase 2', allow '2' to be replaced by 'two'" VAR new_value = "NADH dehydrogenase subunit 2" match1 = "NADH dehydrogenase subunit 2 gene" match2 = "gene" match3 = "2" existing_text = "eReplace" case_sensitive = false ignore_space = true ignore_punctuation = true FOR EACH Protein DO obj = Resolve("data.prot.name") WHERE EQUALS(obj, match1, case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", match1, match2, match3); SetStringQual (obj, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_258 "Apply NADH dehydrogenase subunit 3 to protein name (overwrite existing text) where object text equals 'NADH dehydrogenase subunit 3 gene' (ignore spaces, ignore punctuation), allow 'gene' to be replaced by 'sequence', 'partial sequence', 'complete sequence', 'partial', 'complete', 'gene sequence', and 'protein', allow 'NADH dehydrogenase subunit 3 gene' to be replaced by 'NADH dehydrogenase 3 gene' and 'NADH dehydrogenase 3', allow '3' to be replaced by 'three'" VAR new_value = "NADH dehydrogenase subunit 3" match1 = "NADH dehydrogenase subunit 3 gene" match2 = "gene" match3 = "3" existing_text = "eReplace" case_sensitive = false ignore_space = true ignore_punctuation = true FOR EACH Protein DO obj = Resolve("data.prot.name") WHERE EQUALS(obj, match1, case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", match1, match2, match3); SetStringQual (obj, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_259 "Apply NADH dehydrogenase subunit 4 to protein name (overwrite existing text) where object text equals 'NADH dehydrogenase subunit 4 gene' (ignore spaces, ignore punctuation), allow 'gene' to be replaced by 'sequence', 'partial sequence', 'complete sequence', 'partial', 'complete', 'gene sequence', and 'protein', allow 'NADH dehydrogenase subunit 4 gene' to be replaced by 'NADH dehydrogenase 4 gene' and 'NADH dehydrogenase 4', allow '4' to be replaced by 'four'" VAR new_value = "NADH dehydrogenase subunit 4" match1 = "NADH dehydrogenase subunit 4 gene" match2 = "gene" match3 = "4" existing_text = "eReplace" case_sensitive = false ignore_space = true ignore_punctuation = true FOR EACH Protein DO obj = Resolve("data.prot.name") WHERE EQUALS(obj, match1, case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", match1, match2, match3); SetStringQual (obj, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_260 "Apply NADH dehydrogenase subunit 5 to protein name (overwrite existing text) where object text equals 'NADH dehydrogenase subunit 5 gene' (ignore spaces, ignore punctuation), allow 'gene' to be replaced by 'sequence', 'partial sequence', 'complete sequence', 'partial', 'complete', 'gene sequence', and 'protein', allow 'NADH dehydrogenase subunit 5 gene' to be replaced by 'NADH dehydrogenase 5 gene' and 'NADH dehydrogenase 5', allow '5' to be replaced by 'five'" VAR new_value = "NADH dehydrogenase subunit 5" match1 = "NADH dehydrogenase subunit 5 gene" match2 = "gene" match3 = "5" existing_text = "eReplace" case_sensitive = false ignore_space = true ignore_punctuation = true FOR EACH Protein DO obj = Resolve("data.prot.name") WHERE EQUALS(obj, match1, case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", match1, match2, match3); SetStringQual (obj, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_261 "Apply NADH dehydrogenase subunit 6 to protein name (overwrite existing text) where object text equals 'NADH dehydrogenase subunit 6 gene' (ignore spaces, ignore punctuation), allow 'gene' to be replaced by 'sequence', 'partial sequence', 'complete sequence', 'partial', 'complete', 'gene sequence', and 'protein', allow 'NADH dehydrogenase subunit 6 gene' to be replaced by 'NADH dehydrogenase 6 gene' and 'NADH dehydrogenase 6', allow '6' to be replaced by 'six'" VAR new_value = "NADH dehydrogenase subunit 6" match1 = "NADH dehydrogenase subunit 6 gene" match2 = "gene" match3 = "6" existing_text = "eReplace" case_sensitive = false ignore_space = true ignore_punctuation = true FOR EACH Protein DO obj = Resolve("data.prot.name") WHERE EQUALS(obj, match1, case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", match1, match2, match3); SetStringQual (obj, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_262 "Apply actin to protein name (overwrite existing text) where object text equals 'Actin gene' (ignore spaces, ignore punctuation), allow 'gene' to be replaced by 'sequence', 'partial sequence', 'complete sequence', 'partial', 'complete', 'gene sequence', and 'protein'" VAR new_value = "actin" match = "Actin gene" existing_text = "eReplace" case_sensitive = false ignore_space = true ignore_punctuation = true FOR EACH Protein DO o = Resolve("data.prot.name") WHERE EQUALS(o, match, case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", match); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_263 "Apply alpha-actin to protein name (overwrite existing text) where object text equals 'alpha Actin gene' (ignore spaces, ignore punctuation), allow 'gene' to be replaced by 'sequence', 'partial sequence', 'complete sequence', 'partial', 'complete', 'gene sequence', and 'protein'" VAR new_value = "alpha-actin" match = "alpha Actin gene" existing_text = "eReplace" case_sensitive = false ignore_space = true ignore_punctuation = true FOR EACH Protein DO o = Resolve("data.prot.name") WHERE EQUALS(o, match, case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", match); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_264 "Apply actin to mRNA product (overwrite existing text) where object text equals 'Actin gene' (ignore spaces, ignore punctuation), allow 'gene' to be replaced by 'sequence', 'partial sequence', 'complete sequence', 'partial', 'complete', 'gene sequence', and 'protein'" VAR new_value = "actin" existing_text = "eReplace" match = "Actin gene" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH mRNA WHERE EQUALS("data.rna.ext.name", match, case_sensitive, ignore_spaces, ignore_punctuation, "synonyms.txt", match) DO SetStringQual ("data.rna.ext.name", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_265 "Apply alpha-actin to mRNA product (overwrite existing text) where object text equals 'alpha Actin gene' (ignore spaces, ignore punctuation), allow 'gene' to be replaced by 'sequence', 'partial sequence', 'complete sequence', 'partial', 'complete', 'gene sequence', and 'protein'" VAR new_value = "alpha-actin" existing_text = "eReplace" match = "alpha Actin gene" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH mRNA WHERE EQUALS("data.rna.ext.name", match, case_sensitive, ignore_spaces, ignore_punctuation, "synonyms.txt", match) DO SetStringQual ("data.rna.ext.name", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_266 "Apply hypothetical protein to protein name (overwrite existing text) where object text equals 'Hypothetical protein gene' (ignore spaces, ignore punctuation), allow 'gene' to be replaced by 'sequence', 'partial sequence', 'complete sequence', 'partial', 'complete', and 'gene sequence', allow 'Hypothetical protein gene' to be replaced by 'Hypothetical'" VAR new_value = "hypothetical protein" match = "Hypothetical protein gene" existing_text = "eReplace" case_sensitive = false ignore_space = true ignore_punctuation = true FOR EACH Protein DO o = Resolve("data.prot.name") WHERE EQUALS(o, match, case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", match); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_269 "Edit protein name replace 'Histone H3' (case insensitive) with 'histone H3'" VAR find_text = "Histone H3" repl_text = "histone H3" location = "anywhere" case_sensitive = false FOR EACH Protein DO o = Resolve("data.prot.name"); EditStringQual (o, "", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_270 "Edit mRNA product replace 'Histone H3' (case insensitive) with 'histone H3'" VAR find_text = "Histone H3" repl_text = "histone H3" location = "anywhere" case_sensitive = false FOR EACH mRNA DO EditStringQual ("data.rna.ext.name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_271 "Edit protein name replace 'Putative' (case insensitive) with 'putative'" VAR find_text = "Putative" repl_text = "putative" location = "anywhere" case_sensitive = false FOR EACH Protein DO o = Resolve("data.prot.name"); EditStringQual (o, "", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_272 "Apply putative to protein name (prefix separated by space) where object text ends with ', putative' (ignore spaces, ignore punctuation) and where object text does not start with 'putative' (ignore spaces), allow 'putative' to be replaced by 'hypothetical'" VAR new_value = "putative" existing_text = "ePrepend" delimiter = " " match = ", putative" case_sensitive = false ignore_space = true ignore_punctuation_constr1 = true ignore_punctuation_constr2 = false FOR EACH Protein DO o = Resolve("data.prot.name") WHERE ENDS(o, match, case_sensitive, ignore_space, ignore_punctuation_constr1) AND NOT STARTS(o, "putative", case_sensitive, ignore_space, ignore_punctuation_constr2, "synonyms.txt", "putative"); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_273 "Edit protein name replace ', putative' (case insensitive) with '' where object text starts with 'putative' (ignore spaces, ignore punctuation)" VAR find_text = ", putative" repl_text = " " location = "at the end" case_sensitive = false ignore_space = true ignore_punctuation = true FOR EACH Protein DO o = Resolve("data.prot.name") WHERE STARTS(o, "putative", case_sensitive, ignore_space, ignore_punctuation); EditStringQual (o, "", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_274 "Edit protein name replace ' putative' (case insensitive) with '' where object text starts with 'putative' (ignore spaces, ignore punctuation)" VAR find_text = " putative" repl_text = " " location = "at the end" case_sensitive = false ignore_space = true ignore_punctuation = true FOR EACH Protein DO o = Resolve("data.prot.name") WHERE STARTS(o, "putative", case_sensitive, ignore_space, ignore_punctuation); EditStringQual (o, "", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_275 "Edit protein name replace 'Polymerase' (case insensitive) with 'polymerase' where protein name contains 'Polymerase sequence' (ignore spaces, ignore punctuation), allow 'Polymerase sequence' to be replaced by 'Polymerase', 'Polymerase gene', and 'Polymerase protein'" VAR find_text = "Polymerase" repl_text = "polymerase" location = "anywhere" case_sensitive = false ignore_space = true ignore_punctuation = true match = "Polymerase sequence" FOR EACH Protein DO o = Resolve("data.prot.name") WHERE CONTAINS(o, match, case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", match); EditStringQual (o, "", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_276 "Apply beta-tubulin to protein name (overwrite existing text) where object text equals 'beta-tubulin gene' (ignore spaces, ignore punctuation), allow 'gene' to be replaced by 'sequence', 'partial sequence', 'complete sequence', 'partial', 'complete', 'gene sequence', and 'protein', allow 'beta-tubulin' to be replaced by 'beta tubulin'" VAR new_value = "beta-tubulin" existing_text = "eReplace" match = "beta-tubulin gene" case_sensitive = false ignore_space = true ignore_punctuation = true FOR EACH Protein DO o = Resolve("data.prot.name") WHERE EQUALS(o, match, case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", match); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_277 "Apply beta-tubulin to mRNA product (overwrite existing text) where object text equals 'beta-tubulin gene' (ignore spaces, ignore punctuation), allow 'gene' to be replaced by 'sequence', 'partial sequence', 'complete sequence', 'partial', 'complete', 'gene sequence', and 'protein', allow 'beta-tubulin' to be replaced by 'beta tubulin'" VAR new_value = "beta-tubulin" existing_text = "eReplace" match = "beta-tubulin gene" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH mRNA WHERE EQUALS("data.rna.ext.name", match, case_sensitive, ignore_spaces, ignore_punctuation, "synonyms.txt", match) DO SetStringQual ("data.rna.ext.name", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_278 "Apply beta-actin to protein name (overwrite existing text) where object text equals 'beta-actin gene' (ignore spaces, ignore punctuation), allow 'gene' to be replaced by 'sequence', 'partial sequence', 'complete sequence', 'partial', 'complete', 'gene sequence', and 'protein', allow 'beta-actin' to be replaced by 'beta actin' and 'beta_actin'" VAR new_value = "beta-actin" existing_text = "eReplace" match = "beta-actin gene" match_gene = "gene" case_sensitive = false ignore_space = true ignore_punctuation = true FOR EACH Protein DO o = Resolve("data.prot.name") WHERE EQUALS(o, match, case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", match, match_gene); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_279 "Apply beta-actin to mRNA product (overwrite existing text) where object text equals 'beta-actin gene' (ignore spaces, ignore punctuation), allow 'gene' to be replaced by 'sequence', 'partial sequence', 'complete sequence', 'partial', 'complete', 'gene sequence', and 'protein', allow 'beta-actin' to be replaced by 'beta actin' and 'beta_actin'" VAR new_value = "beta-actin" existing_text = "eReplace" match = "beta-actin gene" match_gene = "gene" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH mRNA WHERE EQUALS("data.rna.ext.name", match, case_sensitive, ignore_spaces, ignore_punctuation, "synonyms.txt", match, match_gene) DO SetStringQual ("data.rna.ext.name", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_284 "Edit rRNA product replace 'S RIBOSOMAL RNA' (case insensitive) with 'S ribosomal RNA' where object text does not end with 'S ribosomal RNA' (case-sensitive)" VAR find_text = "S RIBOSOMAL RNA" repl_text = "S ribosomal RNA" location = "anywhere" case_sensitive = false case_sensitive_constr = true FOR EACH rRNA WHERE NOT ENDS("data.rna.ext.name", repl_text, case_sensitive_constr) DO EditStringQual ("data.rna.ext.name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_285 "Edit rRNA product replace 'ribosomal RNA gene' (case insensitive) with 'ribosomal RNA' where object text contains 'ribosomal RNA gene' (ignore spaces, ignore punctuation), allow 'ribosomal RNA gene' to be replaced by 'ribosomal RNA gene sequence'" VAR find_text = "ribosomal RNA gene" repl_text = "ribosomal RNA" location = "anywhere" case_sensitive = false ignore_space = true ignore_punctuation = true FOR EACH rRNA WHERE CONTAINS("data.rna.ext.name", find_text, case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", find_text) DO EditStringQual ("data.rna.ext.name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_286 "Apply large subunit ribosomal RNA to rRNA product (overwrite existing text) where object text equals 'LSU ribosomal RNA' (ignore spaces, ignore punctuation), allow 'LSU ribosomal RNA' to be replaced by 'large subunit (LSU) ribosomal RNA'" VAR new_value = "large subunit ribosomal RNA" existing_text = "eReplace" match = "LSU ribosomal RNA" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH rRNA WHERE EQUALS("data.rna.ext.name", match, case_sensitive, ignore_spaces, ignore_punctuation, "synonyms.txt", match) DO SetStringQual ("data.rna.ext.name", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_287 "Edit rRNA product replace 'rRNA gene' (case insensitive) with 'ribosomal RNA'" VAR find_text = "rRNA gene" repl_text = "ribosomal RNA" location = "anywhere" case_sensitive = false FOR EACH rRNA DO EditStringQual ("data.rna.ext.name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_288 "Edit rRNA product replace '-rRNA' (case insensitive) with ' ribosomal RNA' where rRNA product does not equal 's-rRNA' (ignore spaces, ignore punctuation) and where rRNA product does not equal 'l-rRNA' (ignore spaces, ignore punctuation)" VAR find_text = "-rRNA" repl_text = " ribosomal RNA" location = "at the end" case_sensitive = false ignore_space = true ignore_punctuation = true FOR EACH rRNA WHERE NOT EQUALS("data.rna.ext.name", "s-rRNA", case_sensitive, ignore_space, ignore_punctuation) AND NOT EQUALS("data.rna.ext.name", "l-rRNA", case_sensitive, ignore_space, ignore_punctuation) DO EditStringQual ("data.rna.ext.name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_289 "Edit rRNA product replace ' S RIBOSOMAL RNA' (case insensitive) with 'S ribosomal RNA'" VAR find_text = " S RIBOSOMAL RNA" repl_text = "S ribosomal RNA" location = "anywhere" case_sensitive = false FOR EACH rRNA DO EditStringQual ("data.rna.ext.name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_290 "Edit rRNA product replace 'Subunit Ribosomal RNA' (case insensitive) with 'subunit ribosomal RNA' where object text does not end with 'subunit ribosomal RNA' (case-sensitive)" VAR find_text = "Subunit Ribosomal RNA" repl_text = "subunit ribosomal RNA" location = "anywhere" case_sensitive_edit = false case_sensitive_constr = true FOR EACH rRNA WHERE NOT ENDS("data.rna.ext.name", repl_text, case_sensitive_constr) DO EditStringQual ("data.rna.ext.name", find_text, repl_text, location, case_sensitive_edit); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_291 "Edit rRNA product replace 'RDNA Gene sequence' (case insensitive) with 'ribosomal RNA'" VAR find_text = "RDNA Gene sequence" repl_text = "ribosomal RNA" location = "anywhere" case_sensitive = false FOR EACH rRNA DO EditStringQual ("data.rna.ext.name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_292 "Apply small subunit ribosomal RNA to rRNA product (overwrite existing text) where object text equals 'SSU ribosomal RNA' (ignore spaces, ignore punctuation), allow 'SSU ribosomal RNA' to be replaced by 'small subunit (SSU) ribosomal RNA'" VAR new_value = "small subunit ribosomal RNA" existing_text = "eReplace" match = "SSU ribosomal RNA" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH rRNA WHERE EQUALS("data.rna.ext.name", match, case_sensitive, ignore_spaces, ignore_punctuation, "synonyms.txt", match) DO SetStringQual ("data.rna.ext.name", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_293 "Edit rRNA product replace 'S SSU ribosomal RNA' (case insensitive) with 'S small subunit ribosomal RNA'" VAR find_text = "S SSU ribosomal RNA" repl_text = "S small subunit ribosomal RNA" location = "at the end" case_sensitive = false FOR EACH rRNA DO EditStringQual ("data.rna.ext.name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_294 "Edit rRNA product replace 'SSU' (case insensitive) with 'small subunit ribosomal RNA' where object text equals 'SSU' (ignore spaces, ignore punctuation)" VAR find_text = "SSU" repl_text = "small subunit ribosomal RNA" location = "at the end" case_sensitive = false ignore_space = true ignore_punctuation = true FOR EACH rRNA WHERE EQUALS("data.rna.ext.name", find_text, case_sensitive, ignore_space, ignore_punctuation) DO EditStringQual ("data.rna.ext.name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_295 "Edit rRNA product replace 'LSU' (case insensitive) with 'large subunit ribosomal RNA' where object text equals 'LSU' (ignore spaces, ignore punctuation)" VAR find_text = "LSU" repl_text = "large subunit ribosomal RNA" location = "at the end" case_sensitive = false ignore_space = true ignore_punctuation = true FOR EACH rRNA WHERE EQUALS("data.rna.ext.name", find_text, case_sensitive, ignore_space, ignore_punctuation) DO EditStringQual ("data.rna.ext.name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_296 "Edit rRNA product replace 'S LSU ribosomal RNA' (case insensitive) with 'S large subunit ribosomal RNA'" VAR find_text = "S LSU ribosomal RNA" repl_text = "S large subunit ribosomal RNA" location = "at the end" case_sensitive = false FOR EACH rRNA DO EditStringQual ("data.rna.ext.name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_297 "Apply 5.8S ribosomal RNA to rRNA product (overwrite existing text) where rRNA product equals '5.8S ribosomal RNA gene' (ignore spaces, ignore punctuation), allow 'RNA' to be replaced by 'DNA', allow 'ribosomal RNA gene' to be replaced by 'ribosomal DNA', 'rDNA', 'RDNA', 'RDAN', 'RNA', 'DNA', 'ribosomal', and 'RNA gene', allow 'gene' to be replaced by 'sequence', 'region', 'gene sequence', 'sequence region', 'gene sequence region', 'partial sequence', 'partial gene sequence', and 'partial', allow '5.8S ribosomal RNA gene' to be replaced by '5.8SrDNA', '5.8SrRNA', '5.8SrDNA gene', '5.8SrRNA gene', '5.8SrDNA gene sequence', '5.8SrRNA gene sequence', '5.8SrDNA gene sequence region', '5.8SrRNA gene sequence region', '5.8S rDNA gene', '5.8S rRNA gene', and '5.8S gene', allow '5.8S ribosomal RNA gene' to be replaced by 'gene 5.8S rRNA' and 'gene 5.8S ribosomal RNA'" VAR new_value = "5.8S ribosomal RNA" existing_text = "eReplace" match1 = "5.8S ribosomal RNA gene" match2 = "ribosomal RNA gene" match3 = "RNA" match4 = "gene" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH rRNA WHERE EQUALS("data.rna.ext.name", match1, case_sensitive, ignore_spaces, ignore_punctuation, "synonyms.txt", match1, match2, match3, match4) DO SetStringQual ("data.rna.ext.name", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_298 "Apply 12S ribosomal RNA to rRNA product (overwrite existing text) where rRNA product equals '12S ribosomal RNA gene' (ignore spaces, ignore punctuation), allow 'RNA' to be replaced by 'DNA', allow 'ribosomal RNA gene' to be replaced by 'ribosomal DNA', 'rDNA', 'RDNA', 'RDAN', 'RNA', 'DNA', 'ribosomal', and 'RNA gene', allow 'gene' to be replaced by 'sequence', 'region', 'gene sequence', 'sequence region', 'gene sequence region', 'partial sequence', 'partial gene sequence', and 'partial', allow '12S ribosomal RNA gene' to be replaced by '12SrDNA', '12SrRNA', '12SrDNA gene', '12SrRNA gene', '12SrDNA gene sequence', '12SrRNA gene sequence', '12SrDNA gene sequence region', '12SrRNA gene sequence region', '12S rDNA gene', and '12S rRNA gene', allow '12S ribosomal RNA gene' to be replaced by 'gene 12S rRNA', 'gene 12S ribosomal RNA', and '12S gene'" VAR new_value = "12S ribosomal RNA" existing_text = "eReplace" match1 = "12S ribosomal RNA gene" match2 = "ribosomal RNA gene" match3 = "RNA" match4 = "gene" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH rRNA WHERE EQUALS("data.rna.ext.name", match1, case_sensitive, ignore_spaces, ignore_punctuation, "synonyms.txt", match1, match2, match3, match4) DO SetStringQual ("data.rna.ext.name", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_299 "Apply 16S ribosomal RNA to rRNA product (overwrite existing text) where rRNA product equals '16S ribosomal RNA gene' (ignore spaces, ignore punctuation), allow 'RNA' to be replaced by 'DNA', allow 'ribosomal RNA gene' to be replaced by 'ribosomal DNA', 'rDNA', 'RDNA', 'RDAN', 'RNA', 'DNA', 'ribosomal', and 'RNA gene', allow 'gene' to be replaced by 'sequence', 'region', 'gene sequence', 'sequence region', 'gene sequence region', 'partial sequence', 'partial gene sequence', and 'partial', allow '16S ribosomal RNA gene' to be replaced by '16SrDNA', '16SrRNA', '16SrDNA gene', '16SrRNA gene', '16SrDNA gene sequence', '16SrRNA gene sequence', '16SrDNA gene sequence region', '16SrRNA gene sequence region', '16S rDNA gene', and '16S rRNA gene', allow '16S ribosomal RNA gene' to be replaced by 'gene 16S rRNA', 'gene 16S ribosomal RNA', and '16S gene'" VAR new_value = "16S ribosomal RNA" existing_text = "eReplace" match1 = "16S ribosomal RNA gene" match2 = "ribosomal RNA gene" match3 = "RNA" match4 = "gene" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH rRNA WHERE EQUALS("data.rna.ext.name", match1, case_sensitive, ignore_spaces, ignore_punctuation, "synonyms.txt", match1, match2, match3, match4) DO SetStringQual ("data.rna.ext.name", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_300 "Apply 18S ribosomal RNA to rRNA product (overwrite existing text) where rRNA product equals '18S ribosomal RNA gene' (ignore spaces, ignore punctuation), allow 'RNA' to be replaced by 'DNA', allow 'ribosomal RNA gene' to be replaced by 'ribosomal DNA', 'rDNA', 'RDNA', 'RDAN', 'RNA', 'DNA', 'ribosomal', and 'RNA gene', allow 'gene' to be replaced by 'sequence', 'region', 'gene sequence', 'sequence region', 'gene sequence region', 'partial sequence', 'partial gene sequence', and 'partial', allow '18S ribosomal RNA gene' to be replaced by '18SrDNA', '18SrRNA', '18SrDNA gene', '18SrRNA gene', '18SrDNA gene sequence', '18SrRNA gene sequence', '18SrDNA gene sequence region', '18SrRNA gene sequence region', '18S rDNA gene', and '18S rRNA gene', allow '18S ribosomal RNA gene' to be replaced by 'gene 18S rRNA', 'gene 18S ribosomal RNA', and '18S gene'" VAR new_value = "18S ribosomal RNA" existing_text = "eReplace" match1 = "18S ribosomal RNA gene" match2 = "ribosomal RNA gene" match3 = "RNA" match4 = "gene" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH rRNA WHERE EQUALS("data.rna.ext.name", match1, case_sensitive, ignore_spaces, ignore_punctuation, "synonyms.txt", match1, match2, match3, match4) DO SetStringQual ("data.rna.ext.name", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_301 "Apply 23S ribosomal RNA to rRNA product (overwrite existing text) where rRNA product equals '23S ribosomal RNA gene' (ignore spaces, ignore punctuation), allow 'RNA' to be replaced by 'DNA', allow 'ribosomal RNA gene' to be replaced by 'ribosomal DNA', 'rDNA', 'RDNA', 'RDAN', 'RNA', 'DNA', 'ribosomal', and 'RNA gene', allow 'gene' to be replaced by 'sequence', 'region', 'gene sequence', 'sequence region', 'gene sequence region', 'partial sequence', 'partial gene sequence', and 'partial', allow '23S ribosomal RNA gene' to be replaced by '23SrDNA', '23SrRNA', '23SrDNA gene', '23SrRNA gene', '23SrDNA gene sequence', '23SrRNA gene sequence', '23SrDNA gene sequence region', '23SrRNA gene sequence region', '23S rDNA gene', and '23S rRNA gene', allow '23S ribosomal RNA gene' to be replaced by 'gene 23S rRNA', 'gene 23S ribosomal RNA', and '23S gene'" VAR new_value = "23S ribosomal RNA" existing_text = "eReplace" match1 = "23S ribosomal RNA gene" match2 = "ribosomal RNA gene" match3 = "RNA" match4 = "gene" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH rRNA WHERE EQUALS("data.rna.ext.name", match1, case_sensitive, ignore_spaces, ignore_punctuation, "synonyms.txt", match1, match2, match3, match4) DO SetStringQual ("data.rna.ext.name", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_302 "Apply 26S ribosomal RNA to rRNA product (overwrite existing text) where rRNA product equals '26S ribosomal RNA gene' (ignore spaces, ignore punctuation), allow 'RNA' to be replaced by 'DNA', allow 'ribosomal RNA gene' to be replaced by 'ribosomal DNA', 'rDNA', 'RDNA', 'RDAN', 'RNA', 'DNA', 'ribosomal', and 'RNA gene', allow 'gene' to be replaced by 'sequence', 'region', 'gene sequence', 'sequence region', 'gene sequence region', 'partial sequence', 'partial gene sequence', and 'partial', allow '26S ribosomal RNA gene' to be replaced by '26SrDNA', '26SrRNA', '26SrDNA gene', '26SrRNA gene', '26SrDNA gene sequence', '26SrRNA gene sequence', '26SrDNA gene sequence region', '26SrRNA gene sequence region', '26S rDNA gene', and '26S rRNA gene', allow '26S ribosomal RNA gene' to be replaced by 'gene 26S rRNA', 'gene 26S ribosomal RNA', and '26S gene'" VAR new_value = "26S ribosomal RNA" existing_text = "eReplace" match1 = "26S ribosomal RNA gene" match2 = "ribosomal RNA gene" match3 = "RNA" match4 = "gene" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH rRNA WHERE EQUALS("data.rna.ext.name", match1, case_sensitive, ignore_spaces, ignore_punctuation, "synonyms.txt", match1, match2, match3, match4) DO SetStringQual ("data.rna.ext.name", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_303 "Apply 28S ribosomal RNA to rRNA product (overwrite existing text) where rRNA product equals '28S ribosomal RNA gene' (ignore spaces, ignore punctuation), allow 'RNA' to be replaced by 'DNA', allow 'ribosomal RNA gene' to be replaced by 'ribosomal DNA', 'rDNA', 'RDNA', 'RDAN', 'RNA', 'DNA', 'ribosomal', and 'RNA gene', allow 'gene' to be replaced by 'sequence', 'region', 'gene sequence', 'sequence region', 'gene sequence region', 'partial sequence', 'partial gene sequence', and 'partial', allow '28S ribosomal RNA gene' to be replaced by '28SrDNA', '28SrRNA', '28SrDNA gene', '28SrRNA gene', '28SrDNA gene sequence', '28SrRNA gene sequence', '28SrDNA gene sequence region', '28SrRNA gene sequence region', '28S rDNA gene', and '28S rRNA gene', allow '28S ribosomal RNA gene' to be replaced by 'gene 28S rRNA', 'gene 28S ribosomal RNA', and '28S gene'" VAR new_value = "28S ribosomal RNA" existing_text = "eReplace" match1 = "28S ribosomal RNA gene" match2 = "ribosomal RNA gene" match3 = "RNA" match4 = "gene" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH rRNA WHERE EQUALS("data.rna.ext.name", match1, case_sensitive, ignore_spaces, ignore_punctuation, "synonyms.txt", match1, match2, match3, match4) DO SetStringQual ("data.rna.ext.name", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_304 "Apply 18S small subunit ribosomal RNA to rRNA product (overwrite existing text) where object text contains '18S SSU ribosomal RNA' (ignore spaces, ignore punctuation), allow '18S SSU ribosomal RNA' to be replaced by '18S small subunit SSU ribosomal RNA', '18S small subunit (SSU) ribosomal RNA', and 'small subunit (SSU) 18S ribosomal RNA'" VAR new_value = "18S small subunit ribosomal RNA" existing_text = "eReplace" match = "18S SSU ribosomal RNA" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH rRNA WHERE CONTAINS("data.rna.ext.name", match, case_sensitive, ignore_spaces, ignore_punctuation, "synonyms.txt", match) DO SetStringQual ("data.rna.ext.name", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_305 "Apply 28S large subunit ribosomal RNA to rRNA product (overwrite existing text) where object text contains '28S LSU ribosomal RNA' (ignore spaces, ignore punctuation), allow '28S LSU ribosomal RNA' to be replaced by '28S large subunit LSU ribosomal RNA', '28S large subunit (LSU) ribosomal RNA', and 'large subunit (LSU) 28S ribosomal RNA'" VAR new_value = "28S large subunit ribosomal RNA" existing_text = "eReplace" match = "28S LSU ribosomal RNA" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH rRNA WHERE EQUALS("data.rna.ext.name", match, case_sensitive, ignore_spaces, ignore_punctuation, "synonyms.txt", match) DO SetStringQual ("data.rna.ext.name", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_309 "Edit Any RNA comment replace 'spaser' (case insensitive) with 'spacer'" VAR find_text = "spaser" repl_text = "spacer" location = "anywhere" case_sensitive = false FOR EACH SeqFeat WHERE CHOICETYPE("data") = "rna" DO EditStringQual ("comment", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_310 "Edit Any RNA comment replace 'intrenal' (case insensitive) with 'internal'" VAR find_text = "intrenal" repl_text = "internal" location = "anywhere" case_sensitive = false FOR EACH SeqFeat WHERE CHOICETYPE("data") = "rna" DO EditStringQual ("comment", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_311 "Edit Any RNA comment replace 'trascribed' (case insensitive) with 'transcribed'" VAR find_text = "trascribed" repl_text = "transcribed" location = "anywhere" case_sensitive = false FOR EACH SeqFeat WHERE CHOICETYPE("data") = "rna" DO EditStringQual ("comment", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_318 "Edit misc_RNA comment replace '18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and 28S ribosomal RNA gene, partial sequence' (case insensitive) with 'contains 18S ribosomal RNA, internal transcribed spacer 1, 5.8S ribosomal RNA, internal transcribed spacer 2, and 28S ribosomal RNA'" VAR find_text = "18S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, 5.8S ribosomal RNA gene, and internal transcribed spacer 2, complete sequence; and 28S ribosomal RNA gene, partial sequence" repl_text = "contains 18S ribosomal RNA, internal transcribed spacer 1, 5.8S ribosomal RNA, internal transcribed spacer 2, and 28S ribosomal RNA" location = "at the beginning" case_sensitive = false FOR EACH MiscRNA DO EditStringQual ("comment", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_350 "Edit protein name replace 'recombination activating gene' (case insensitive) with 'recombination activating protein'" VAR find_text = "recombination activating gene" repl_text = "recombination activating protein" location = "anywhere" case_sensitive = false FOR EACH Protein DO o = Resolve("data.prot.name"); EditStringQual (o, "", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_351 "Edit protein name replace 'recombination-activating gene' (case insensitive) with 'recombination activating protein'" VAR find_text = "recombination-activating gene" repl_text = "recombination activating protein" location = "anywhere" case_sensitive = false FOR EACH Protein DO o = Resolve("data.prot.name"); EditStringQual (o, "", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_352 "Edit protein name replace 'recombination-activating protein' (case insensitive) with 'recombination activating protein'" VAR find_text = "recombination-activating protein" repl_text = "recombination activating protein" location = "anywhere" case_sensitive = false FOR EACH Protein DO o = Resolve("data.prot.name"); EditStringQual (o, "", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_353 "Edit protein name replace 'recombination activating protein, partial gene' (case insensitive) with 'recombination activating protein'" VAR find_text = "recombination activating protein, partial gene" repl_text = "recombination activating protein" location = "anywhere" case_sensitive = false FOR EACH Protein DO o = Resolve("data.prot.name"); EditStringQual (o, "", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_354 "Apply gag to gene locus (overwrite existing text) where gene locus equals 'GAG gene' (ignore spaces, ignore punctuation), allow 'gene' to be replaced by 'sequence' and where source taxname starts with 'Human immunodeficiency virus' (ignore spaces, ignore punctuation)" VAR new_value = "gag" existing_text = "eReplace" match = "GAG gene" case_sensitive = false ignore_space = true ignore_punctuation = true start_match = "Human immunodeficiency virus" FOR EACH Gene WHERE EQUALS("data.gene.locus", match, case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", match) AND STARTS(BIOSOURCE_FOR_SEQFEAT("org.taxname"), start_match, case_sensitive, ignore_space, ignore_punctuation) DO SetStringQual ("data.gene.locus", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_355 "Apply pol to gene locus (overwrite existing text) where gene locus equals 'POL gene' (ignore spaces, ignore punctuation), allow 'gene' to be replaced by 'sequence' and where source taxname starts with 'Human immunodeficiency virus' (ignore spaces, ignore punctuation)" VAR new_value = "pol" existing_text = "eReplace" match = "POL gene" case_sensitive = false ignore_space = true ignore_punctuation = true start_match = "Human immunodeficiency virus" FOR EACH Gene WHERE EQUALS("data.gene.locus", match, case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", match) AND STARTS(BIOSOURCE_FOR_SEQFEAT("org.taxname"), start_match, case_sensitive, ignore_space, ignore_punctuation) DO SetStringQual ("data.gene.locus", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_356 "Apply vif to gene locus (overwrite existing text) where gene locus equals 'VIF gene' (ignore spaces, ignore punctuation), allow 'gene' to be replaced by 'sequence' and where source taxname starts with 'Human immunodeficiency virus' (ignore spaces, ignore punctuation)" VAR new_value = "vif" existing_text = "eReplace" match = "VIF gene" case_sensitive = false ignore_space = true ignore_punctuation = true start_match = "Human immunodeficiency virus" FOR EACH Gene WHERE EQUALS("data.gene.locus", match, case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", match) AND STARTS(BIOSOURCE_FOR_SEQFEAT("org.taxname"), start_match, case_sensitive, ignore_space, ignore_punctuation) DO SetStringQual ("data.gene.locus", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_357 "Apply vpr to gene locus (overwrite existing text) where gene locus equals 'VPR gene' (ignore spaces, ignore punctuation), allow 'gene' to be replaced by 'sequence' and where source taxname starts with 'Human immunodeficiency virus' (ignore spaces, ignore punctuation)" VAR new_value = "vpr" existing_text = "eReplace" match = "VPR gene" case_sensitive = false ignore_space = true ignore_punctuation = true start_match = "Human immunodeficiency virus" FOR EACH Gene WHERE EQUALS("data.gene.locus", match, case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", match) AND STARTS(BIOSOURCE_FOR_SEQFEAT("org.taxname"), start_match, case_sensitive, ignore_space, ignore_punctuation) DO SetStringQual ("data.gene.locus", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_358 "Apply tat to gene locus (overwrite existing text) where gene locus equals 'TAT gene' (ignore spaces, ignore punctuation), allow 'gene' to be replaced by 'sequence' and where source taxname starts with 'Human immunodeficiency virus' (ignore spaces, ignore punctuation)" VAR new_value = "tat" existing_text = "eReplace" match = "TAT gene" case_sensitive = false ignore_space = true ignore_punctuation = true start_match = "Human immunodeficiency virus" FOR EACH Gene WHERE EQUALS("data.gene.locus", match, case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", match) AND STARTS(BIOSOURCE_FOR_SEQFEAT("org.taxname"), start_match, case_sensitive, ignore_space, ignore_punctuation) DO SetStringQual ("data.gene.locus", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_359 "Apply rev to gene locus (overwrite existing text) where gene locus equals 'REV gene' (ignore spaces, ignore punctuation), allow 'gene' to be replaced by 'sequence' and where source taxname starts with 'Human immunodeficiency virus' (ignore spaces, ignore punctuation)" VAR new_value = "rev" existing_text = "eReplace" match = "REV gene" case_sensitive = false ignore_space = true ignore_punctuation = true start_match = "Human immunodeficiency virus" FOR EACH Gene WHERE EQUALS("data.gene.locus", match, case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", match) AND STARTS(BIOSOURCE_FOR_SEQFEAT("org.taxname"), start_match, case_sensitive, ignore_space, ignore_punctuation) DO SetStringQual ("data.gene.locus", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_360 "Apply vpu to gene locus (overwrite existing text) where gene locus equals 'VPU gene' (ignore spaces, ignore punctuation), allow 'gene' to be replaced by 'sequence' and where source taxname starts with 'Human immunodeficiency virus' (ignore spaces, ignore punctuation)" VAR new_value = "vpu" existing_text = "eReplace" match = "VPU gene" case_sensitive = false ignore_space = true ignore_punctuation = true start_match = "Human immunodeficiency virus" FOR EACH Gene WHERE EQUALS("data.gene.locus", match, case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", match) AND STARTS(BIOSOURCE_FOR_SEQFEAT("org.taxname"), start_match, case_sensitive, ignore_space, ignore_punctuation) DO SetStringQual ("data.gene.locus", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_361 "Apply env to gene locus (overwrite existing text) where gene locus equals 'ENV gene' (ignore spaces, ignore punctuation), allow 'gene' to be replaced by 'sequence' and where source taxname starts with 'Human immunodeficiency virus' (ignore spaces, ignore punctuation)" VAR new_value = "env" existing_text = "eReplace" match = "ENV gene" case_sensitive = false ignore_space = true ignore_punctuation = true start_match = "Human immunodeficiency virus" FOR EACH Gene WHERE EQUALS("data.gene.locus", match, case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", match) AND STARTS(BIOSOURCE_FOR_SEQFEAT("org.taxname"), start_match, case_sensitive, ignore_space, ignore_punctuation) DO SetStringQual ("data.gene.locus", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_362 "Apply nef to gene locus (overwrite existing text) where gene locus equals 'NEF gene' (ignore spaces, ignore punctuation), allow 'gene' to be replaced by 'sequence' and where source taxname starts with 'Human immunodeficiency virus' (ignore spaces, ignore punctuation)" VAR new_value = "nef" existing_text = "eReplace" match = "NEF gene" case_sensitive = false ignore_space = true ignore_punctuation = true start_match = "Human immunodeficiency virus" FOR EACH Gene WHERE EQUALS("data.gene.locus", match, case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", match) AND STARTS(BIOSOURCE_FOR_SEQFEAT("org.taxname"), start_match, case_sensitive, ignore_space, ignore_punctuation) DO SetStringQual ("data.gene.locus", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_363 "Apply gag protein to CDS product (overwrite existing text) where CDS product equals 'gag sequence' (ignore spaces, ignore punctuation), allow 'sequence' to be replaced by 'gene', allow 'gag' to be replaced by 'Gag protein', allow 'gag sequence' to be replaced by 'gag' and 'Gag protein' and where source taxname starts with 'Human immunodeficiency virus' (ignore spaces, ignore punctuation)" VAR new_value = "gag protein" existing_text = "eReplace" match = "gag sequence" case_sensitive = false ignore_space = true ignore_punctuation = true taxname = "Human immunodeficiency virus" FOR EACH Protein WHERE STARTS(BIOSOURCE_FOR_SEQFEAT("org.taxname"), taxname, case_sensitive, ignore_space, ignore_punctuation) DO o = Resolve("data.prot.name") WHERE EQUALS(o, match, case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", match); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_364 "Apply pol protein to CDS product (overwrite existing text) where CDS product equals 'pol sequence' (ignore spaces, ignore punctuation), allow 'sequence' to be replaced by 'gene', allow 'pol' to be replaced by 'Pol protein', allow 'pol sequence' to be replaced by 'pol' and 'pol protein' and where source taxname starts with 'Human immunodeficiency virus' (ignore spaces, ignore punctuation)" VAR new_value = "pol protein" existing_text = "eReplace" match = "pol sequence" case_sensitive = false ignore_space = true ignore_punctuation = true taxname = "Human immunodeficiency virus" FOR EACH Protein WHERE STARTS(BIOSOURCE_FOR_SEQFEAT("org.taxname"), taxname, case_sensitive, ignore_space, ignore_punctuation) DO o = Resolve("data.prot.name") WHERE EQUALS(o, match, case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", match); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_365 "Apply vif protein to CDS product (overwrite existing text) where CDS product equals 'vif' (ignore spaces, ignore punctuation), allow '' to be replaced by 'sequence' and 'gene', allow 'vif' to be replaced by 'Vif protein' and where source taxname starts with 'Human immunodeficiency virus' (ignore spaces, ignore punctuation)" VAR new_value = "vif protein" existing_text = "eReplace" match = "vif sequence" case_sensitive = false ignore_space = true ignore_punctuation = true taxname = "Human immunodeficiency virus" FOR EACH Protein WHERE STARTS(BIOSOURCE_FOR_SEQFEAT("org.taxname"), taxname, case_sensitive, ignore_space, ignore_punctuation) DO o = Resolve("data.prot.name") WHERE EQUALS(o, match, case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", match); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_366 "Apply vpr protein to CDS product (overwrite existing text) where CDS product equals 'vpr sequence' (ignore spaces, ignore punctuation), allow 'sequence' to be replaced by 'gene', allow 'vpr' to be replaced by 'Vpr protein', allow 'vpr sequence' to be replaced by 'vpr' and 'Vpr protein' and where source taxname starts with 'Human immunodeficiency virus' (ignore spaces, ignore punctuation)" VAR new_value = "vpr protein" existing_text = "eReplace" match = "vpr sequence" case_sensitive = false ignore_space = true ignore_punctuation = true taxname = "Human immunodeficiency virus" FOR EACH Protein WHERE STARTS(BIOSOURCE_FOR_SEQFEAT("org.taxname"), taxname, case_sensitive, ignore_space, ignore_punctuation) DO o = Resolve("data.prot.name") WHERE EQUALS(o, match, case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", match); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_367 "Apply tat protein to CDS product (overwrite existing text) where CDS product equals 'tat sequence' (ignore spaces, ignore punctuation), allow 'sequence' to be replaced by 'gene', allow 'tat' to be replaced by 'Tat protein', allow 'tat sequence' to be replaced by 'tat' and 'Tat protein' and where source taxname starts with 'Human immunodeficiency virus' (ignore spaces, ignore punctuation)" VAR new_value = "tat protein" existing_text = "eReplace" match = "tat sequence" case_sensitive = false ignore_space = true ignore_punctuation = true taxname = "Human immunodeficiency virus" FOR EACH Protein WHERE STARTS(BIOSOURCE_FOR_SEQFEAT("org.taxname"), taxname, case_sensitive, ignore_space, ignore_punctuation) DO o = Resolve("data.prot.name") WHERE EQUALS(o, match, case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", match); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_368 "Apply rev protein to CDS product (overwrite existing text) where CDS product equals 'rev sequence' (ignore spaces, ignore punctuation), allow 'sequence' to be replaced by 'gene', allow 'rev' to be replaced by 'Rev protein', allow 'rev sequence' to be replaced by 'rev' and 'Rev protein' and where source taxname starts with 'Human immunodeficiency virus' (ignore spaces, ignore punctuation)" VAR new_value = "rev protein" existing_text = "eReplace" match = "rev sequence" case_sensitive = false ignore_space = true ignore_punctuation = true taxname = "Human immunodeficiency virus" FOR EACH Protein WHERE STARTS(BIOSOURCE_FOR_SEQFEAT("org.taxname"), taxname, case_sensitive, ignore_space, ignore_punctuation) DO o = Resolve("data.prot.name") WHERE EQUALS(o, match, case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", match); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_369 "Apply vpu protein to CDS product (overwrite existing text) where CDS product equals 'vpu sequence' (ignore spaces, ignore punctuation), allow 'sequence' to be replaced by 'gene', allow 'vpu' to be replaced by 'Vpu protein', allow 'vpu sequence' to be replaced by 'vpu' and 'Vpu protein' and where source taxname starts with 'Human immunodeficiency virus' (ignore spaces, ignore punctuation)" VAR new_value = "vpu protein" existing_text = "eReplace" match = "vpu sequence" case_sensitive = false ignore_space = true ignore_punctuation = true taxname = "Human immunodeficiency virus" FOR EACH Protein WHERE STARTS(BIOSOURCE_FOR_SEQFEAT("org.taxname"), taxname, case_sensitive, ignore_space, ignore_punctuation) DO o = Resolve("data.prot.name") WHERE EQUALS(o, match, case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", match); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_370 "Apply envelope glycoprotein to CDS product (overwrite existing text) where CDS product equals 'env sequence' (ignore spaces, ignore punctuation), allow 'env' to be replaced by 'envelope', allow 'sequence' to be replaced by 'gene', allow 'env sequence' to be replaced by 'Env protein', 'Env glycoprotein', and 'Env' and where source taxname starts with 'Human immunodeficiency virus' (ignore spaces, ignore punctuation)" VAR new_value = "envelope glycoprotein" existing_text = "eReplace" match = "env sequence" case_sensitive = false ignore_space = true ignore_punctuation = true taxname = "Human immunodeficiency virus" FOR EACH Protein WHERE STARTS(BIOSOURCE_FOR_SEQFEAT("org.taxname"), taxname, case_sensitive, ignore_space, ignore_punctuation) DO o = Resolve("data.prot.name") WHERE EQUALS(o, match, case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", match); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_371 "Apply nef protein to CDS product (overwrite existing text) where CDS product equals 'nef sequence' (ignore spaces, ignore punctuation), allow 'sequence' to be replaced by 'gene', allow 'nef sequence' to be replaced by 'Nef protein' and 'nef' and where source taxname starts with 'Human immunodeficiency virus' (ignore spaces, ignore punctuation)" VAR new_value = "nef protein" existing_text = "eReplace" match = "nef sequence" case_sensitive = false ignore_space = true ignore_punctuation = true taxname = "Human immunodeficiency virus" FOR EACH Protein WHERE STARTS(BIOSOURCE_FOR_SEQFEAT("org.taxname"), taxname, case_sensitive, ignore_space, ignore_punctuation) DO o = Resolve("data.prot.name") WHERE EQUALS(o, match, case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", match); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_372 "Apply envelope protein to CDS product (overwrite existing text) where CDS product equals 'Envelope protein sequence' (ignore spaces, ignore punctuation), allow 'sequence' to be replaced by 'gene', allow 'Envelope protein sequence' to be replaced by 'Envelope protein'" VAR new_value = "envelope protein" existing_text = "eReplace" match = "Envelope protein sequence" case_sensitive = false ignore_space = true ignore_punctuation = true FOR EACH Protein DO o = Resolve("data.prot.name") WHERE EQUALS(o, match, case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", match); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_373 "Apply polyprotein to protein name (overwrite existing text) where object text equals 'Polyprotein gene' (ignore spaces, ignore punctuation), allow 'Polyprotein gene' to be replaced by 'Polyprotein', 'polyprotein sequence', 'polyprotein cds', 'poliprotein', 'pollyprotein', and 'polliprotein'" VAR new_value = "polyprotein" existing_text = "eReplace" match = "Polyprotein gene" case_sensitive = false ignore_space = true ignore_punctuation = true FOR EACH Protein DO o = Resolve("data.prot.name") WHERE EQUALS(o, match, case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", match); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_374 "Apply glycoprotein to CDS product (overwrite existing text) where CDS product equals 'Glycoprotein sequence' (ignore spaces, ignore punctuation), allow 'sequence' to be replaced by 'gene', allow 'Glycoprotein sequence' to be replaced by 'Glycoprotein'" VAR new_value = "glycoprotein" existing_text = "eReplace" match = "Glycoprotein sequence" case_sensitive = false ignore_space = true ignore_punctuation = true FOR EACH Protein DO o = Resolve("data.prot.name") WHERE EQUALS(o, match, case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", match); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_375 "Apply nucleoprotein to CDS product (overwrite existing text) where CDS product equals 'Nucleoprotein sequence' (ignore spaces, ignore punctuation), allow 'sequence' to be replaced by 'gene', allow 'Nucleoprotein sequence' to be replaced by 'Nucleoprotein'" VAR new_value = "nucleoprotein" existing_text = "eReplace" match = "Nucleoprotein sequence" case_sensitive = false ignore_space = true ignore_punctuation = true FOR EACH Protein DO o = Resolve("data.prot.name") WHERE EQUALS(o, match, case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", match); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_376 "Apply coat protein to CDS product (overwrite existing text) where CDS product equals 'Coat protein sequence' (ignore spaces, ignore punctuation), allow 'sequence' to be replaced by 'gene', allow 'Coat protein sequence' to be replaced by 'Coat protein'" VAR new_value = "coat protein" existing_text = "eReplace" match = "Coat protein sequence" case_sensitive = false ignore_space = true ignore_punctuation = true FOR EACH Protein DO o = Resolve("data.prot.name") WHERE EQUALS(o, match, case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", match); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_377 "Apply capsid protein to CDS product (overwrite existing text) where CDS product equals 'Capsid protein sequence' (ignore spaces, ignore punctuation), allow 'sequence' to be replaced by 'gene', allow 'Capsid protein sequence' to be replaced by 'capside protein', 'capside protein sequence', and 'Capsid protein'" VAR new_value = "capsid protein" existing_text = "eReplace" match = "Capsid protein sequence" case_sensitive = false ignore_space = true ignore_punctuation = true FOR EACH Protein DO o = Resolve("data.prot.name") WHERE EQUALS(o, match, case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", match); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_378 "Apply movement protein to CDS product (overwrite existing text) where CDS product equals 'movement protein sequence' (ignore spaces, ignore punctuation), allow 'sequence' to be replaced by 'gene', allow 'movement protein sequence' to be replaced by 'Movement protein'" VAR new_value = "movement protein" existing_text = "eReplace" match = "movement protein sequence" case_sensitive = false ignore_space = true ignore_punctuation = true FOR EACH Protein DO o = Resolve("data.prot.name") WHERE EQUALS(o, match, case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", match); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_379 "Apply envelope glycoprotein to CDS product (overwrite existing text) where CDS product equals 'Envelope glycoprotein sequence' (ignore spaces, ignore punctuation), allow 'sequence' to be replaced by 'gene', allow 'Envelope glycoprotein sequence' to be replaced by 'Envelope glycoprotein protein' and 'Envelope glycoprotein'" VAR new_value = "envelope glycoprotein" existing_text = "eReplace" match = "Envelope glycoprotein sequence" case_sensitive = false ignore_space = true ignore_punctuation = true FOR EACH Protein DO o = Resolve("data.prot.name") WHERE EQUALS(o, match, case_sensitive, ignore_space, ignore_punctuation, "synonyms.txt", match); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_380 "Apply nonstructural protein to protein name (overwrite existing text) where object text equals 'Nonstructural protein' (ignore spaces, ignore punctuation)" VAR new_value = "nonstructural protein" existing_text = "eReplace" match = "Nonstructural protein" case_sensitive = false ignore_space = true ignore_punctuation = true FOR EACH Protein DO o = Resolve("data.prot.name") WHERE EQUALS(o, match, case_sensitive, ignore_space, ignore_punctuation); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_381 "Apply RNA-dependent RNA polymerase to protein name (overwrite existing text) where object text equals 'RNA-Dependent RNA polymerase' (ignore spaces, ignore punctuation)" VAR new_value = "RNA-dependent RNA polymerase" existing_text = "eReplace" match = "RNA-Dependent RNA polymerase" case_sensitive = false ignore_space = true ignore_punctuation = true FOR EACH Protein DO o = Resolve("data.prot.name") WHERE EQUALS(o, match, case_sensitive, ignore_space, ignore_punctuation); SetStringQual (o, "", new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_386 "Remove location plastid where source lineage contains 'Bacteria' (case-sensitive) and where source dbxref starts with 'taxon:' (case-sensitive)" VAR qual_name = "genome" match_text = "Bacteria" case_sensitive = true FOR EACH BioSource WHERE genome = "plastid" AND CONTAINS("org.orgname.lineage", match_text, case_sensitive) AND STARTS("org.db.db", "taxon", case_sensitive) Do RemoveQual(qual_name); Done ------------------------------------------------------------------------------ MACRO Autofix_macro_387 "Remove location chloroplast where source lineage contains 'Bacteria' (case-sensitive) and where source dbxref starts with 'taxon:' (case-sensitive)" VAR qual_name = "genome" match_text = "Bacteria" case_sensitive = true FOR EACH BioSource WHERE genome = "chloroplast" AND CONTAINS("org.orgname.lineage", match_text, case_sensitive) AND STARTS("org.db.db", "taxon", case_sensitive) Do RemoveQual(qual_name); Done ------------------------------------------------------------------------------ MACRO Autofix_macro_388 "Remove location chromoplast where source lineage contains 'Bacteria' (case-sensitive) and where source dbxref starts with 'taxon:' (case-sensitive)" VAR qual_name = "genome" match_text = "Bacteria" case_sensitive = true FOR EACH BioSource WHERE genome = "chromoplast" AND CONTAINS("org.orgname.lineage", match_text, case_sensitive) AND STARTS("org.db.db", "taxon", case_sensitive) Do RemoveQual(qual_name); Done ------------------------------------------------------------------------------ MACRO Autofix_macro_389 "Remove location leucoplast where source lineage contains 'Bacteria' (case-sensitive) and where source dbxref starts with 'taxon:' (case-sensitive)" VAR qual_name = "genome" match_text = "Bacteria" case_sensitive = true FOR EACH BioSource WHERE genome = "leucoplast" AND CONTAINS("org.orgname.lineage", match_text, case_sensitive) AND STARTS("org.db.db", "taxon", case_sensitive) Do RemoveQual(qual_name); Done ------------------------------------------------------------------------------ MACRO Autofix_macro_390 "Remove location proplastid where source lineage contains 'Bacteria' (case-sensitive) and where source dbxref starts with 'taxon:' (case-sensitive)" VAR qual_name = "genome" match_text = "Bacteria" case_sensitive = true FOR EACH BioSource WHERE genome = "proplastid" AND CONTAINS("org.orgname.lineage", match_text, case_sensitive) AND STARTS("org.db.db", "taxon", case_sensitive) Do RemoveQual(qual_name); Done ------------------------------------------------------------------------------ MACRO Autofix_macro_391 "Remove location plastid where source lineage contains 'Archaea' (case-sensitive) and where source dbxref starts with 'taxon:' (case-sensitive)" VAR qual_name = "genome" match_text = "Archaea" case_sensitive = true FOR EACH BioSource WHERE genome = "plastid" AND CONTAINS("org.orgname.lineage", match_text, case_sensitive) AND STARTS("org.db.db", "taxon", case_sensitive) Do RemoveQual(qual_name); Done ------------------------------------------------------------------------------ MACRO Autofix_macro_392 "Remove location chloroplast where source lineage contains 'Archaea' (case-sensitive) and where source dbxref starts with 'taxon:' (case-sensitive)" VAR qual_name = "genome" match_text = "Archaea" case_sensitive = true FOR EACH BioSource WHERE genome = "chloroplast" AND CONTAINS("org.orgname.lineage", match_text, case_sensitive) AND STARTS("org.db.db", "taxon", case_sensitive) Do RemoveQual(qual_name); Done ------------------------------------------------------------------------------ MACRO Autofix_macro_393 "Remove location chromoplast where source lineage contains 'Archaea' (case-sensitive) and where source dbxref starts with 'taxon:' (case-sensitive)" VAR qual_name = "genome" match_text = "Archaea" case_sensitive = true FOR EACH BioSource WHERE genome = "chromoplast" AND CONTAINS("org.orgname.lineage", match_text, case_sensitive) AND STARTS("org.db.db", "taxon", case_sensitive) Do RemoveQual(qual_name); Done ------------------------------------------------------------------------------ MACRO Autofix_macro_394 "Remove location leucoplast where source lineage contains 'Archaea' (case-sensitive) and where source dbxref starts with 'taxon:' (case-sensitive)" VAR qual_name = "genome" match_text = "Archaea" case_sensitive = true FOR EACH BioSource WHERE genome = "leucoplast" AND CONTAINS("org.orgname.lineage", match_text, case_sensitive) AND STARTS("org.db.db", "taxon", case_sensitive) Do RemoveQual(qual_name); Done ------------------------------------------------------------------------------ MACRO Autofix_macro_395 "Remove location proplastid where source lineage contains 'Archaea' (case-sensitive) and where source dbxref starts with 'taxon:' (case-sensitive)" VAR qual_name = "genome" match_text = "Archaea" case_sensitive = true FOR EACH BioSource WHERE genome = "proplastid" AND CONTAINS("org.orgname.lineage", match_text, case_sensitive) AND STARTS("org.db.db", "taxon", case_sensitive) Do RemoveQual(qual_name); Done ------------------------------------------------------------------------------ MACRO Autofix_macro_396 "Remove location mitochondrion where source lineage contains 'Bacteria' (case-sensitive) and where source dbxref starts with 'taxon:' (case-sensitive)" VAR qual_name = "genome" match_text = "Bacteria" case_sensitive = true FOR EACH BioSource WHERE genome = "mitochondrion" AND CONTAINS("org.orgname.lineage", match_text, case_sensitive) AND STARTS("org.db.db", "taxon", case_sensitive) Do RemoveQual(qual_name); Done ------------------------------------------------------------------------------ MACRO Autofix_macro_397 "Remove location mitochondrion where source lineage contains 'Archaea' (case-sensitive) and where source dbxref starts with 'taxon:' (case-sensitive)" VAR qual_name = "genome" match_text = "Archaea" case_sensitive = true FOR EACH BioSource WHERE genome = "mitochondrion" AND CONTAINS("org.orgname.lineage", match_text, case_sensitive) AND STARTS("org.db.db", "taxon", case_sensitive) Do RemoveQual(qual_name); Done ------------------------------------------------------------------------------ MACRO Autofix_macro_398 "Remove location extrachromosomal where source lineage contains 'Viruses' (case-sensitive) and where source dbxref starts with 'taxon:' (case-sensitive)" VAR qual_name = "genome" match_text = "Viruses" case_sensitive = true FOR EACH BioSource WHERE genome = "extrachromosomal" AND CONTAINS("org.orgname.lineage", match_text, case_sensitive) AND STARTS("org.db.db", "taxon", case_sensitive) Do RemoveQual(qual_name); Done ------------------------------------------------------------------------------ MACRO Autofix_macro_404 "Edit collected-by replace ':' with ','" VAR find_text = ":" repl_text = "," location = "anywhere" case_sensitive = true FOR EACH BioSource DO o = Resolve("subtype") WHERE o.subtype = "collected-by"; EditStringQual (o, "name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_405 "Edit identified-by replace ':' with ','" VAR find_text = ":" repl_text = "," location = "anywhere" case_sensitive = true FOR EACH BioSource DO o = Resolve("subtype") WHERE o.subtype = "identified-by"; EditStringQual (o, "name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_406 "Edit collected-by replace '/' with ','" VAR find_text = "/" repl_text = "," location = "anywhere" case_sensitive = true FOR EACH BioSource DO o = Resolve("subtype") WHERE o.subtype = "collected-by"; EditStringQual (o, "name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_407 "Edit identified-by replace '/' with ','" VAR find_text = "/" repl_text = "," location = "anywhere" case_sensitive = true FOR EACH BioSource DO o = Resolve("subtype") WHERE o.subtype = "identified-by"; EditStringQual (o, "name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_408 "Edit collected-by replace ';' with ','" VAR find_text = ";" repl_text = "," location = "anywhere" case_sensitive = true FOR EACH BioSource DO o = Resolve("subtype") WHERE o.subtype = "collected-by"; EditStringQual (o, "name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_409 "Edit identified-by replace ';' with ','" VAR find_text = ";" repl_text = "," location = "anywhere" case_sensitive = true FOR EACH BioSource DO o = Resolve("subtype") WHERE o.subtype = "identified-by"; EditStringQual (o, "name", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_411 "Edit misc_feature note replace 'Control region' (case insensitive) with 'control region' where object text equals 'Control region' (ignore punctuation)" VAR find_text = "Control region" repl_text = "control region" location = "anywhere" case_sensitive = false ignore_spaces = false ignore_punctuation = true FOR EACH Misc_feat WHERE EQUALS("comment", find_text, case_sensitive, ignore_spaces, ignore_punctuation) DO EditStringQual ("comment", find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_428 "Edit taxname replace 'uncultured fungus clone' (case insensitive) with 'uncultured fungus' where source taxname equals 'uncultured fungus clone' (ignore spaces, ignore punctuation)" VAR qual_name = "org.taxname" find_text = "uncultured fungus clone" repl_text = "uncultured fungus" location = "anywhere" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH BioSource WHERE EQUALS(qual_name, find_text, case_sensitive, ignore_spaces, ignore_punctuation) DO EditStringQual (qual_name, find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_429 "Edit taxname replace 'uncultured bacteria clone' (case insensitive) with 'uncultured bacterium' where source taxname equals 'uncultured bacteria clone' (ignore spaces, ignore punctuation)" VAR qual_name = "org.taxname" find_text = "uncultured bacteria clone" repl_text = "uncultured bacterium" location = "anywhere" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH BioSource WHERE EQUALS(qual_name, find_text, case_sensitive, ignore_spaces, ignore_punctuation) DO EditStringQual (qual_name, find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_430 "Edit taxname replace 'uncultured bacterium clone' (case insensitive) with 'uncultured bacterium' where source taxname equals 'uncultured bacterium clone' (ignore spaces, ignore punctuation)" VAR qual_name = "org.taxname" find_text = "uncultured bacterium clone" repl_text = "uncultured bacterium" location = "anywhere" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH BioSource WHERE EQUALS(qual_name, find_text, case_sensitive, ignore_spaces, ignore_punctuation) DO EditStringQual (qual_name, find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_431 "Edit taxname replace 'unculture bacterium' (case insensitive) with 'uncultured bacterium' where source taxname contains 'unculture bacterium' (ignore spaces, ignore punctuation)" VAR qual_name = "org.taxname" find_text = "unculture bacterium" repl_text = "uncultured bacterium" location = "anywhere" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH BioSource WHERE EQUALS(qual_name, find_text, case_sensitive, ignore_spaces, ignore_punctuation) DO EditStringQual (qual_name, find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_432 "Edit taxname replace 'unculture fungus' (case insensitive) with 'uncultured fungus' where source taxname contains 'unculture fungus' (ignore spaces, ignore punctuation)" VAR qual_name = "org.taxname" find_text = "unculture fungus" repl_text = "uncultured fungus" location = "anywhere" case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH BioSource WHERE EQUALS(qual_name, find_text, case_sensitive, ignore_spaces, ignore_punctuation) DO EditStringQual (qual_name, find_text, repl_text, location, case_sensitive); DONE ------------------------------------------------------------------------------ MACRO Autofix_macro_433 "Edit taxname replace 'Measles viruse' with 'Measles virus' where source taxname equals 'Measles viruse' (ignore spaces, ignore punctuation)" VAR qual_name = "org.taxname" find_text = "Measles viruse" repl_text = "Measles virus" location = "anywhere" case_sensitive_edit = true case_sensitive = false ignore_spaces = true ignore_punctuation = true FOR EACH BioSource WHERE EQUALS(qual_name, find_text, case_sensitive, ignore_spaces, ignore_punctuation) DO EditStringQual (qual_name, find_text, repl_text, location, case_sensitive_edit); DONE ------------------------------------------------------------------------------ MACRO Flu_segment_macro_01 "Apply 4 to segment (overwrite existing text) where gene locus equals 'HA' (case-sensitive)" VAR qual_name = "subtype" modifier = "segment" new_value = "4" existing_text = "eReplace" case_sensitive = true FOR EACH BioSource WHERE EQUALS(FEATURES_FOR_BIOSOURCE("gene", "data.gene.locus"), "HA", case_sensitive) DO obj = Resolve(qual_name) WHERE obj.subtype = modifier; SetModifier(obj, qual_name, modifier, new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Flu_segment_macro_02 "Apply 1 to segment (overwrite existing text) where gene locus equals 'PB2' (case-sensitive)" VAR qual_name = "subtype" modifier = "segment" new_value = "1" existing_text = "eReplace" case_sensitive = true FOR EACH BioSource WHERE EQUALS(FEATURES_FOR_BIOSOURCE("gene", "data.gene.locus"), "PB2", case_sensitive) DO obj = Resolve(qual_name) WHERE obj.subtype = modifier; SetModifier(obj, qual_name, modifier, new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Flu_segment_macro_03 "Apply 2 to segment (overwrite existing text) where gene locus equals 'PB1' (case-sensitive)" VAR qual_name = "subtype" modifier = "segment" new_value = "2" existing_text = "eReplace" case_sensitive = true FOR EACH BioSource WHERE EQUALS(FEATURES_FOR_BIOSOURCE("gene", "data.gene.locus"), "PB1", case_sensitive) DO obj = Resolve(qual_name) WHERE obj.subtype = modifier; SetModifier(obj, qual_name, modifier, new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Flu_segment_macro_04 "Apply 3 to segment (overwrite existing text) where gene locus equals 'PA' (case-sensitive)" VAR qual_name = "subtype" modifier = "segment" new_value = "3" existing_text = "eReplace" case_sensitive = true FOR EACH BioSource WHERE EQUALS(FEATURES_FOR_BIOSOURCE("gene", "data.gene.locus"), "PA", case_sensitive) DO obj = Resolve(qual_name) WHERE obj.subtype = modifier; SetModifier(obj, qual_name, modifier, new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Flu_segment_macro_05 "Apply 5 to segment (overwrite existing text) where gene locus equals 'NP' (case-sensitive)" VAR qual_name = "subtype" modifier = "segment" new_value = "5" existing_text = "eReplace" case_sensitive = true FOR EACH BioSource WHERE EQUALS(FEATURES_FOR_BIOSOURCE("gene", "data.gene.locus"), "NP", case_sensitive) DO obj = Resolve(qual_name) WHERE obj.subtype = modifier; SetModifier(obj, qual_name, modifier, new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Flu_segment_macro_06 "Apply 6 to segment (overwrite existing text) where gene locus equals 'NA' (case-sensitive)" VAR qual_name = "subtype" modifier = "segment" new_value = "6" existing_text = "eReplace" case_sensitive = true FOR EACH BioSource WHERE EQUALS(FEATURES_FOR_BIOSOURCE("gene", "data.gene.locus"), "NA", case_sensitive) DO obj = Resolve(qual_name) WHERE obj.subtype = modifier; SetModifier(obj, qual_name, modifier, new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Flu_segment_macro_07 "Apply 8 to segment (overwrite existing text) where gene locus starts with 'NS' (case-sensitive)" VAR qual_name = "subtype" modifier = "segment" new_value = "8" existing_text = "eReplace" case_sensitive = true FOR EACH BioSource WHERE EQUALS(FEATURES_FOR_BIOSOURCE("gene", "data.gene.locus"), "NS", case_sensitive) DO obj = Resolve(qual_name) WHERE obj.subtype = modifier; SetModifier(obj, qual_name, modifier, new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO Flu_segment_macro_08 "Apply 7 to segment (overwrite existing text) where gene locus starts with 'M' (case-sensitive)" VAR qual_name = "subtype" modifier = "segment" new_value = "7" existing_text = "eReplace" case_sensitive = true FOR EACH BioSource WHERE EQUALS(FEATURES_FOR_BIOSOURCE("gene", "data.gene.locus"), "M", case_sensitive) DO obj = Resolve(qual_name) WHERE obj.subtype = modifier; SetModifier(obj, qual_name, modifier, new_value, existing_text); DONE ------------------------------------------------------------------------------ MACRO GB_mitomacro_001 "Edit CDS product replace 'NADH dehydrogenase 1' with 'NADH dehydrogenase subunit 1'" VAR find_text = "NADH dehydrogenase 1" repl_text = "NADH dehydrogenase subunit 1" location = "anywhere" case_sensitive = true FOR EACH Protein DO EditStringQual("data.prot.name", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_002 "Edit CDS product replace 'NADH dehydrogenase 2' with 'NADH dehydrogenase subunit 2'" VAR find_text = "NADH dehydrogenase 2" repl_text = "NADH dehydrogenase subunit 2" location = "anywhere" case_sensitive = true FOR EACH Protein DO EditStringQual("data.prot.name", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_003 "Edit CDS product replace 'NADH dehydrogenase 3' with 'NADH dehydrogenase subunit 3'" VAR find_text = "NADH dehydrogenase 3" repl_text = "NADH dehydrogenase subunit 3" location = "anywhere" case_sensitive = true FOR EACH Protein DO EditStringQual("data.prot.name", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_004 "Edit CDS product replace 'NADH dehydrogenase 4' with 'NADH dehydrogenase subunit 4'" VAR find_text = "NADH dehydrogenase 4" repl_text = "NADH dehydrogenase subunit 4" location = "anywhere" case_sensitive = true FOR EACH Protein DO EditStringQual("data.prot.name", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_005 "Edit protein name replace 'NADH dehydrogenase 4L' with 'NADH dehydrogenase subunit 4L'" VAR find_text = "NADH dehydrogenase 4L" repl_text = "NADH dehydrogenase subunit 4L" location = "anywhere" case_sensitive = true FOR EACH Protein DO EditStringQual("data.prot.name", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_006 "Edit protein name replace 'NADH dehydrogenase 5' with 'NADH dehydrogenase subunit 5'" VAR find_text = "NADH dehydrogenase 5" repl_text = "NADH dehydrogenase subunit 5" location = "anywhere" case_sensitive = true FOR EACH Protein DO EditStringQual("data.prot.name", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_007 "Edit CDS product replace 'NADH dehydrogenase 6' with 'NADH dehydrogenase subunit 6'" VAR find_text = "NADH dehydrogenase 6" repl_text = "NADH dehydrogenase subunit 6" location = "anywhere" case_sensitive = true FOR EACH Protein DO EditStringQual("data.prot.name", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_008 "Edit protein name replace 'ND' with 'NADH dehydrogenase subunit '" VAR find_text = "ND" repl_text = "NADH dehydrogenase subunit " location = "anywhere" case_sensitive = true FOR EACH Protein DO EditStringQual("data.prot.name", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_009 "Edit gene locus replace 'NADH dehydrogenase subunit ' with 'ND'" VAR find_text = "NADH dehydrogenase subunit " repl_text = "ND" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_010 "Edit gene locus replace 'nad' with 'ND'" VAR find_text = "nad" repl_text = "ND" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_011 "Edit gene locus replace 'NADH' with 'ND'" VAR find_text = "NADH" repl_text = "ND" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_012 "Edit gene locus replace 'NAD' with 'ND'" VAR find_text = "NAD" repl_text = "ND" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_013 "Edit gene locus replace 'ND4l' with 'ND4L'" VAR find_text = "ND4l" repl_text = "ND4L" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_014 "Edit gene locus replace 'nd' (case insensitive) with 'ND'" VAR find_text = "nd" repl_text = "ND" location = "anywhere" case_sensitive = false FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_015 "Edit protein name replace 'cytochrome oxidase' with 'cytochrome c oxidase'" VAR find_text = "cytochrome oxidase" repl_text = "cytochrome c oxidase" location = "anywhere" case_sensitive = true FOR EACH Protein DO EditStringQual("data.prot.name", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_016 "Edit CDS product replace 'Cytochrome' with 'cytochrome'" VAR find_text = "Cytochrome" repl_text = "cytochrome" location = "anywhere" case_sensitive = true FOR EACH Protein DO EditStringQual("data.prot.name", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_017 "Edit CDS product replace 'oxydase' with 'oxidase'" VAR find_text = "oxydase" repl_text = "oxidase" location = "anywhere" case_sensitive = true FOR EACH Protein DO EditStringQual("data.prot.name", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_018 "Edit CDS product replace 'cytochrome C' with 'cytochrome c'" VAR find_text = "cytochrome C" repl_text = "cytochrome c" location = "at the beginning" case_sensitive = false FOR EACH Protein DO EditStringQual("data.prot.name", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_019 "Edit CDS product replace 'cytochrome c oxidase subunit 1' with 'cytochrome c oxidase subunit I'" VAR find_text = "cytochrome c oxidase subunit 1" repl_text = "cytochrome c oxidase subunit I" location = "at the end" case_sensitive = true FOR EACH Protein DO EditStringQual("data.prot.name", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_020 "Edit CDS product replace 'cytochrome c oxidase subunit 2' with 'cytochrome c oxidase subunit II'" VAR find_text = "cytochrome c oxidase subunit 2" repl_text = "cytochrome c oxidase subunit II" location = "at the end" case_sensitive = true FOR EACH Protein DO EditStringQual("data.prot.name", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_021 "Edit CDS product replace 'cytochrome c oxidase subunit 3' with 'cytochrome c oxidase subunit III'" VAR find_text = "cytochrome c oxidase subunit 3" repl_text = "cytochrome c oxidase subunit III" location = "at the end" case_sensitive = true FOR EACH Protein DO EditStringQual("data.prot.name", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_022 "Edit gene locus replace 'cytochrome c oxidase subunit ' (case insensitive) with 'COX'" VAR find_text = "cytochrome c oxidase subunit " repl_text = "COX" location = "anywhere" case_sensitive = false FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_023 "Edit gene locus replace 'cox' with 'COX'" VAR find_text = "cox" repl_text = "COX" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_024 "Edit gene locus replace 'CO1' with 'COX1'" VAR find_text = "CO1" repl_text = "COX1" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_025 "Edit gene locus replace 'CO2' with 'COX2'" VAR find_text = "CO2" repl_text = "COX2" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_026 "Edit gene locus replace 'CO3' with 'COX3'" VAR find_text = "CO3" repl_text = "COX3" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_027 "Edit gene locus replace 'COXiii' with 'COX3'" VAR find_text = "COXiii" repl_text = "COX3" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_028 "Edit gene locus replace 'COXi' with 'COX1'" VAR find_text = "COXi" repl_text = "COX1" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_029 "Edit gene locus replace 'COXii' with 'COX2'" VAR find_text = "COXii" repl_text = "COX2" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_030 "Edit gene locus replace 'COXIII' with 'COX3'" VAR find_text = "COXIII" repl_text = "COX3" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_031 "Edit gene locus replace 'COXII' with 'COX2'" VAR find_text = "COXII" repl_text = "COX2" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_032 "Edit gene locus replace 'cox1' with 'COX1'" VAR find_text = "cox1" repl_text = "COX1" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_033 "Edit gene locus replace 'coxI' with 'COX1'" VAR find_text = "coxI" repl_text = "COX1" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_034 "Apply COI to gene synonym (overwrite existing text) where gene locus equals 'COI' (case-sensitive)" VAR case_sensitive = true FOR EACH Gene WHERE EQUALS("data.gene.locus", "COI", case_sensitive) DO SetStringQual("data.gene.syn", "COI", "eReplace"); DONE -------------------------------------------------------------- MACRO GB_mitomacro_035 "Apply COX1 to gene locus (overwrite existing text) where gene locus equals 'COI' (case-sensitive)" VAR case_sensitive = true FOR EACH Gene WHERE EQUALS("data.gene.locus", "COI", case_sensitive) DO SetStringQual("data.gene.locus", "COX1", "eReplace"); DONE -------------------------------------------------------------- MACRO GB_mitomacro_036 "Apply COII to gene synonym (overwrite existing text) where gene locus equals 'COII' (case-sensitive)" VAR case_sensitive = true FOR EACH Gene WHERE EQUALS("data.gene.locus", "COII", case_sensitive) DO SetStringQual("data.gene.syn", "COII", "eReplace"); DONE -------------------------------------------------------------- MACRO GB_mitomacro_037 "Apply COIII to gene synonym (overwrite existing text) where gene locus equals 'COIII' (case-sensitive)" VAR case_sensitive = true FOR EACH Gene WHERE EQUALS("data.gene.locus", "COIII", case_sensitive) DO SetStringQual("data.gene.syn", "COIII", "eReplace"); DONE -------------------------------------------------------------- MACRO GB_mitomacro_038 "Apply COX3 to gene locus (overwrite existing text) where gene locus equals 'COIII' (case-sensitive)" VAR case_sensitive = true FOR EACH Gene WHERE EQUALS("data.gene.locus", "COIII", case_sensitive) DO SetStringQual("data.gene.locus", "COX3", "eReplace"); DONE -------------------------------------------------------------- MACRO GB_mitomacro_039 "Apply COX2 to gene locus (overwrite existing text) where gene locus equals 'COII' (case-sensitive)" VAR case_sensitive = true FOR EACH Gene WHERE EQUALS("data.gene.locus", "COII", case_sensitive) DO SetStringQual("data.gene.locus", "COX2", "eReplace"); DONE -------------------------------------------------------------- MACRO GB_mitomacro_040 "Edit protein name replace 'COIII' with 'cytochrome c oxidase subunit 3'" VAR find_text = "COIII" repl_text = "cytochrome c oxidase subunit 3" location = "anywhere" case_sensitive = true FOR EACH Protein DO EditStringQual("data.prot.name", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_041 "Edit protein name replace 'COII' with 'cytochrome c oxidase subunit 2'" VAR find_text = "COII" repl_text = "cytochrome c oxidase subunit 2" location = "anywhere" case_sensitive = true FOR EACH Protein DO EditStringQual("data.prot.name", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_042 "Edit protein name replace 'COX1' with 'cytochrome c oxidase subunit I'" VAR find_text = "COX1" repl_text = "cytochrome c oxidase subunit I" location = "anywhere" case_sensitive = true FOR EACH Protein DO EditStringQual("data.prot.name", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_043 "Edit protein name replace 'COX2' with 'cytochrome c oxidase subunit II'" VAR find_text = "COX2" repl_text = "cytochrome c oxidase subunit II" location = "anywhere" case_sensitive = true FOR EACH Protein DO EditStringQual("data.prot.name", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_044 "Edit protein name replace 'COX3' with 'cytochrome c oxidase subunit III'" VAR find_text = "COX3" repl_text = "cytochrome c oxidase subunit III" location = "anywhere" case_sensitive = true FOR EACH Protein DO EditStringQual("data.prot.name", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_045 "Edit protein name replace 'cox' with 'cytochrome c oxidase subunit '" VAR find_text = "cox" repl_text = "cytochrome c oxidase subunit " location = "anywhere" case_sensitive = true FOR EACH Protein DO EditStringQual("data.prot.name", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_046 "Edit protein name replace 'Cox' with 'cytochrome c oxidase subunit '" VAR find_text = "Cox" repl_text = "cytochrome c oxidase subunit " location = "anywhere" case_sensitive = true FOR EACH Protein DO EditStringQual("data.prot.name", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_047 "Edit protein name replace 'COI' with 'cytochrome c oxidase subunit 1'" VAR find_text = "COI" repl_text = "cytochrome c oxidase subunit 1" location = "anywhere" case_sensitive = true FOR EACH Protein DO EditStringQual("data.prot.name", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_048 "Edit gene locus replace 'COXI' with 'COX1'" VAR find_text = "COXI" repl_text = "COX1" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_049 "Edit gene locus replace 'cytb' with 'CYTB'" VAR find_text = "cytb" repl_text = "CYTB" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_050 "Edit gene locus replace 'COB' with 'CYTB'" VAR find_text = "COB" repl_text = "CYTB" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_051 "Edit gene locus replace 'cob' with 'CYTB'" VAR find_text = "cob" repl_text = "CYTB" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_052 "Edit gene locus replace 'nad' with 'ND'" VAR find_text = "nad" repl_text = "ND" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_053 "Edit gene locus replace 'Cox' with 'COX'" VAR find_text = "Cox" repl_text = "COX" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_054 "Edit gene locus replace 'Nad' with 'ND'" VAR find_text = "Nad" repl_text = "ND" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_055 "Edit gene locus replace 'Cox' with 'COX'" VAR find_text = "Cox" repl_text = "COX" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_056 "Edit gene locus replace 'cyt b' with 'CYTB'" VAR find_text = "cyt b" repl_text = "CYTB" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_057 "Edit gene locus replace 'cox' with 'COX'" VAR find_text = "cox" repl_text = "COX" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_058 "Edit gene locus replace 'nad' with 'ND'" VAR find_text = "nad" repl_text = "ND" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_059 "Edit gene locus replace 'cytochrome b' (case insensitive) with 'CYTB'" VAR find_text = "cytochrome b" repl_text = "CYTB" location = "anywhere" case_sensitive = false FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_060 "Edit gene locus replace 'Cytb' (case insensitive) with 'CYTB'" VAR find_text = "Cytb" repl_text = "CYTB" location = "anywhere" case_sensitive = false FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_061 "Edit protein name replace 'COB' with 'cytochrome b'" VAR find_text = "COB" repl_text = "cytochrome b" location = "anywhere" case_sensitive = true FOR EACH Protein DO EditStringQual("data.prot.name", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_062 "Edit CDS product replace 'cytochrome B' with 'cytochrome b'" VAR find_text = "cytochrome B" repl_text = "cytochrome b" location = "at the beginning" case_sensitive = true FOR EACH Protein DO EditStringQual("data.prot.name", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_063 "Edit protein name replace 'apocytochrome b' with 'cytochrome b'" VAR find_text = "apocytochrome b" repl_text = "cytochrome b" location = "anywhere" case_sensitive = true FOR EACH Protein DO EditStringQual("data.prot.name", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_064 "Edit protein name replace 'Cytb' with 'cytochrome b'" VAR find_text = "Cytb" repl_text = "cytochrome b" location = "anywhere" case_sensitive = true FOR EACH Protein DO EditStringQual("data.prot.name", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_065 "Edit protein name replace 'cytB' with 'cytochrome b'" VAR find_text = "cytB" repl_text = "cytochrome b" location = "anywhere" case_sensitive = true FOR EACH Protein DO EditStringQual("data.prot.name", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_066 "Edit gene locus replace 'ATP synthase F0 subunit' with 'ATP'" VAR find_text = "ATP synthase F0 subunit" repl_text = "ATP" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_067 "Edit gene locus replace 'atp' with 'ATP'" VAR find_text = "atp" repl_text = "ATP" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_068 "Edit protein name replace 'atp' with 'ATP synthase F0 subunit '" VAR find_text = "atp" repl_text = "ATP synthase F0 subunit " location = "anywhere" case_sensitive = true FOR EACH Protein DO EditStringQual("data.prot.name", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_069 "Edit protein name replace 'cytb' with 'cytochrome b'" VAR find_text = "cytb" repl_text = "cytochrome b" location = "anywhere" case_sensitive = true FOR EACH Protein DO EditStringQual("data.prot.name", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_070 "Edit protein name replace 'ATPase subunit 6' with 'ATP synthase F0 subunit 6'" VAR find_text = "ATPase subunit 6" repl_text = "ATP synthase F0 subunit 6" location = "anywhere" case_sensitive = true FOR EACH Protein DO EditStringQual("data.prot.name", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_071 "Edit gene locus replace 'ATP ' with 'ATP'" VAR find_text = "ATP " repl_text = "ATP" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_072 "Edit gene locus replace 'ATPase' with 'ATP'" VAR find_text = "ATPase" repl_text = "ATP" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_073 "Edit protein name replace 'ATP8' with 'ATP synthase F0 subunit 8'" VAR find_text = "ATP8" repl_text = "ATP synthase F0 subunit 8" location = "anywhere" case_sensitive = true FOR EACH Protein DO EditStringQual("data.prot.name", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_074 "Edit protein name replace 'ATP6' with 'ATP synthase F0 subunit 6'" VAR find_text = "ATP6" repl_text = "ATP synthase F0 subunit 6" location = "anywhere" case_sensitive = true FOR EACH Protein DO EditStringQual("data.prot.name", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_075 "Edit protein name replace 'CYTB' with 'cytochrome b'" VAR find_text = "CYTB" repl_text = "cytochrome b" location = "anywhere" case_sensitive = true FOR EACH Protein DO EditStringQual("data.prot.name", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_076 "Edit protein name replace 'ATPase subunit 8' with 'ATP synthase F0 subunit 8'" VAR find_text = "ATPase subunit 8" repl_text = "ATP synthase F0 subunit 8" location = "anywhere" case_sensitive = true FOR EACH Protein DO EditStringQual("data.prot.name", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_077 "Edit CDS product replace 'ATP synthase subunit 6' with 'ATP synthase F0 subunit 6'" VAR find_text = "ATP synthase subunit 6" repl_text = "ATP synthase F0 subunit 6" location = "anywhere" case_sensitive = true FOR EACH Protein DO EditStringQual("data.prot.name", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_078 "Edit protein name replace 'Nad' with 'NADH dehydrogenase subunit '" VAR find_text = "Nad" repl_text = "NADH dehydrogenase subunit " location = "anywhere" case_sensitive = true FOR EACH Protein DO EditStringQual("data.prot.name", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_079 "Edit CDS product replace 'ATP synthase subunit 8' with 'ATP synthase F0 subunit 8'" VAR find_text = "ATP synthase subunit 8" repl_text = "ATP synthase F0 subunit 8" location = "anywhere" case_sensitive = true FOR EACH Protein DO EditStringQual("data.prot.name", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_080 "Edit gene locus replace 'tRNA-Ile' with 'trnI'" VAR find_text = "tRNA-Ile" repl_text = "trnI" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_081 "Edit gene locus replace 'tRNA-Lys' with 'trnK'" VAR find_text = "tRNA-Lys" repl_text = "trnK" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_082 "Edit gene locus replace 'tRNA-Leu' with 'trnL'" VAR find_text = "tRNA-Leu" repl_text = "trnL" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_083 "Edit gene locus replace 'tRNA-Ser' with 'trnS'" VAR find_text = "tRNA-Ser" repl_text = "trnS" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_084 "Edit gene locus replace 'tRNA-Trp' with 'trnW'" VAR find_text = "tRNA-Trp" repl_text = "trnW" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_085 "Edit gene locus replace 'tRNA-Cys' with 'trnC'" VAR find_text = "tRNA-Cys" repl_text = "trnC" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_086 "Edit gene locus replace 'tRNA-Gly' with 'trnG'" VAR find_text = "tRNA-Gly" repl_text = "trnG" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_087 "Edit gene locus replace 'tRNA-Asn' with 'trnN'" VAR find_text = "tRNA-Asn" repl_text = "trnN" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_088 "Edit gene locus replace 'tRNA-Asp' with 'trnD'" VAR find_text = "tRNA-Asp" repl_text = "trnD" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_089 "Edit gene locus replace 'tRNA-Thr' with 'trnT'" VAR find_text = "tRNA-Thr" repl_text = "trnT" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_090 "Edit gene locus replace 'tRNA-Pro' with 'trnP'" VAR find_text = "tRNA-Pro" repl_text = "trnP" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_091 "Edit gene locus replace 'tRNA-Arg' with 'trnR'" VAR find_text = "tRNA-Arg" repl_text = "trnR" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_092 "Edit gene locus replace 'tRNA-Gln' with 'trnQ'" VAR find_text = "tRNA-Gln" repl_text = "trnQ" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_093 "Edit gene locus replace 'tRNA-Tyr' with 'trnY'" VAR find_text = "tRNA-Tyr" repl_text = "trnY" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_094 "Edit gene locus replace 'tRNA-Glu' with 'trnE'" VAR find_text = "tRNA-Glu" repl_text = "trnE" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_095 "Edit gene locus replace 'tRNA-Val' with 'trnV'" VAR find_text = "tRNA-Val" repl_text = "trnV" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_096 "Edit gene locus replace 'tRNA-Ala' with 'trnA'" VAR find_text = "tRNA-Ala" repl_text = "trnA" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_097 "Edit gene locus replace 'tRNA-His' with 'trnH'" VAR find_text = "tRNA-His" repl_text = "trnH" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_098 "Edit gene locus replace 'tRNA-Phe' with 'trnF'" VAR find_text = "tRNA-Phe" repl_text = "trnF" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE -------------------------------------------------------------- MACRO GB_mitomacro_099 "Edit gene locus replace 'tRNA-Met' with 'trnM'" VAR find_text = "tRNA-Met" repl_text = "trnM" location = "anywhere" case_sensitive = true FOR EACH Gene DO EditStringQual("data.gene.locus", find_text, repl_text, location, case_sensitive); DONE --------------------------------------------------------------