MODULE flat2asn $$ FORMAT, 1 $^ NonAsciiChar, 1, SEV_ERROR # This is a comment REJECT(LANL,EMBL,DDBJ,PIR,SP) No column of any block of the flat file in any of the formats is allowed to have a nonASCII character. NonASCII is defined as anything greater than decimal value 126 (`~`) or less than decimal 32 (space) except decimal 10, which is a newline. $^ MissingEnd, 2, SEV_ERROR The // line was not found after sequence was found before a line with an letter was found. Likely to be a truncated entry. $^ MissingField, 3, SEV_ERROR Required field was not found in the flat file $^ LocusLinePosition, 4, SEV_ERROR The GenBank flat file format requires fixed column positions for a variety of fields. The following are the fields and the columns that are expected: bp 31-32 literally, "bp" Strand 34-36 This must be blank or ss-, ds-, ms-}; Molecule type 37-40 This must be blank or DNA , RNA , pre-mRNA, mRNA, rRNA, tRNA, uRNA, or scRNA. Topology 43-52 Circular, may be specified or it may be blank ("Tandem???") Division 53-55 Legal division codes are: PRI, ROD, MAM, VRT, INV, PLN, BCT, RNA, VRL, PHG, SYN, UNA, or EST. (blank???) New or mispelled Embl divisions will be reported with a DIVISION_NewDivCode error code. Note that EMBL uses FUN. Date 63-73, and be in dd-mmm-yyyy format. $^ DirSubMode, 5, SEV_WARNING Not standard EMBL format, used in DirSubMode only $^ LineTypeOrder, 6, SEV_WARNING $^ MissingSequenceData, 7, SEV_ERROR $^ ContigWithSequenceData, 8, SEV_ERROR $^ MissingContigFeature, 9, SEV_ERROR $^ MissingSourceFeature, 10, SEV_ERROR $^ MultipleCopyright, 11, SEV_WARNING $^ MissingCopyright, 12, SEV_ERROR $^ MultiplePatRefs, 13, SEV_ERROR $$ DATACLASS, 2 $^ UnKnownClass, 1, SEV_WARNING Swissprot error, only standard and preliminary are allowed. $$ ENTRY, 3 $^ ParsingComplete, 2, SEV_INFO $^ Begin, 3, SEV_ERROR Looking for valid begining according to -f arguement in command line: LOCUS for GenBank; ID for EMBL; ENTRY for PIR; $^ Skipped, 6, SEV_ERROR $^ Repeated, 7, SEV_WARNING $^ LongSequence, 8, SEV_ERROR $^ THC_Sequence, 9, SEV_WARNING $^ Parsed, 10, SEV_INFO $^ ParsingSetup, 11, SEV_INFO $^ GBBlock_not_Empty, 12, SEV_WARNING $^ LongHTGSSequence, 13, SEV_WARNING $$ DATE, 5 $^ IllegalDate, 2, SEV_WARNING Date not in dd-mmm-yyy format $$ SEQUENCE, 7 $^ UnknownBaseHTG3, 1, SEV_WARNING $^ SeqLenNotEq, 2, SEV_WARNING The declared length of the sequence in the record was not equal to the acutal number of residues found. $^ BadResidue, 3, SEV_ERROR Depending upon whether nucleic acid or protein, there are different single letter legal codes. $^ BadData, 4, SEV_WARNING Can't parse the entry because of bad sequence data. $$ SEGMENT, 8 $^ MissSegEntry, 1, SEV_ERROR The Segmented set (GenBank) that is declared has some missing members. That is, if there 6 members declared, The set might only have: 1 of 6, 2 of 6, 4 of 6, 5 of 6 and 6 of 6, and thus be missing 3 of 6. Another possible problem is there could be a line: "3 of 5", instad of "3 of 6" $^ DiffMolType, 2, SEV_WARNING A segmented set is supposed to be from the same molecule, but with some unknown regions. It should therefore all be of the same type of molecule. For this error to occur, there have to be different molecule types for different segments within the set. $^ BadLocusName, 3, SEV_ERROR For GenBank in a segmented set, it is an error if the segment number can not be found at the end of the LOCUS name. So a LOCUS name in SEGMENT 2 of 10 must end in 02, as ABCD02. $^ IncompSeg, 4, SEV_ERROR There were not three blank-separated token on the SEGMENT line, in GenBank Flat File format, the segment line has to look like: SEGMENT 4 of 14 for example. $^ PubMatch, 5, SEV_WARNING There were matching reference with different serial numbers in segments. $^ OnlyOneMember, 6, SEV_WARNING $^ Rejected, 7, SEV_WARNING $$ ACCESSION, 9 $^ BadAccessNum, 2, SEV_ERROR Accession must be upper case letter followed by 5 digits. $^ NoAccessNum, 3, SEV_ERROR No accession number could be found for this entry. The line number given is only approximate. $^ MoreAccessLine, 4, SEV_INFO More than one accession block was found. Continuation lines with the wrong format can cause this in GenBank format. $^ ForeignAccessNum, 5, SEV_WARNING $$ LOCUS, 10 $^ WrongTopology, 2, SEV_WARNING This message occurs when looking for either Circular or 'RNA' or 'DNA' in embl mode. Anything other than this will cause this warning. $^ NoGIBBModMolType, 3, SEV_WARNING In the flat files, the only legal values are blank, RNA, pre-mRNA, mRNA, rRNA, tRNA, uRNA, ss-RNA, ds-RNA, ms-RNA, scRNA, DNA, ds-DNA, and ss-DNA $^ MayBeNewSpeciesCode, 4, SEV_WARNING Swiss-Prot specific error. The species is not in the list of LOCUS name prefix-species pairs. $^ NoSpeciesCode, 5, SEV_WARNING Swiss-Prot error when no species can be found. $^ NoMolType, 6, SEV_WARNING Can't find Molecule type $^ BadLocusName, 7, SEV_ERROR There are multiple possible ways to get this error message. In all formats, this identifier must have either digits or uppercase letters. For Swiss-Prot, the rules are more complicated: Locus name consists of up to 10 uppercase alphanumeric characters rule: X_Y format X is a mnemonic code, up to 4 alphanumeric characters to represent the protein name. Y is a mnemonic species identification code of at most 5 alphanumeric characters to representing the biological source of the protein $^ NoLocusName, 8, SEV_ERROR No token after 'LOCUS' found in GenBank format. $^ NonViralRNAMoltype, 9, SEV_ERROR $$ ORGANISM, 11 $^ NoOrganism, 1, SEV_WARNING EMBL: no OS line found GenBank: No ORGANISM line in the SOURCE block. This message might repeat which trying to guess genetic code. $^ HybridOrganism, 2, SEV_WARNING In EMBL format only, can have multiple organisms (OS blocks). If the taxonomy changes (OC block), this warning is produced. $^ Unclassified, 3, SEV_WARNING $^ MissParen, 4, SEV_WARNING In EMBL format missing parenthesis after common name $^ UnknownReplace, 5, SEV_INFO $^ DoesntMatchFeats, 6, SEV_ERROR $$ KEYWORD, 12 $^ MultipleHTGPhases, 1, SEV_ERROR $^ ESTSubstring, 2, SEV_WARNING $^ STSSubstring, 3, SEV_WARNING $^ GSSSubstring, 4, SEV_WARNING $$ DIVISION, 13 $^ NewDivCode, 1, SEV_WARNING EMBL only (GenBank format related error is a FORMAT.LocusLinePosition error), and the legal codes are: FUN, INV, MAM, ORG, PHG, PLN, PRI, PRO, ROD, SYN, UNA, VRL, VRT, and UNC (UNA == UNC) $^ MappedtoEST, 2, SEV_INFO KW line maps one of these words: "EST", "EST PROTO((expressed sequence tag)", "expressed sequence tag", "partial cDNA sequence", "transcribed sequence fragment", "TSR", "putatively transcribed partial sequence", "UK putts" }; GB-block.div becomes "EST" $^ MappedtoPAT, 3, SEV_WARNING $^ MappedtoSTS, 4, SEV_WARNING $^ Mismatch, 5, SEV_WARNING $^ MissingESTKeywords, 6, SEV_WARNING $^ MissingSTSKeywords, 7, SEV_WARNING $^ MissingPatentRef, 8, SEV_WARNING $^ PATHasESTKeywords, 9, SEV_WARNING $^ PATHasSTSKeywords, 10, SEV_WARNING $^ PATHasCDSFeature, 11, SEV_INFO $^ STSHasCDSFeature, 12, SEV_WARNING $^ NotMappedtoSTS, 13, SEV_WARNING $^ ESTHasSTSKeywords, 14, SEV_INFO $^ ESTHasCDSFeature, 15, SEV_WARNING $^ NotMappedtoEST, 16, SEV_WARNING $^ ShouldBeHTG, 17, SEV_ERROR $^ MissingGSSKeywords, 18, SEV_INFO $^ GSSHasCDSFeature, 19, SEV_WARNING $^ NotMappedtoGSS, 20, SEV_WARNING $^ MappedtoGSS, 21, SEV_WARNING $^ PATHasGSSKeywords, 22, SEV_WARNING $^ LongESTSequence, 23, SEV_WARNING $^ LongSTSSequence, 24, SEV_WARNING $^ LongGSSSequence, 25, SEV_WARNING $^ GBBlockDivision, 26, SEV_WARNING $^ MappedtoCON, 27, SEV_WARNING $^ MissingHTGKeywords, 28, SEV_WARNING $^ ShouldNotBeHTG, 29, SEV_ERROR $^ ConDivInSegset, 30, SEV_ERROR $^ ConDivLacksContig, 31, SEV_WARNING $^ WrongHTGKeyword, 32, SEV_ERROR $$ DEFINITION, 15 $^ HTGNotInProgress, 1, SEV_WARNING $^ DifferingRnaTokens, 2, SEV_WARNING $^ HTGShouldBeComplete, 3, SEV_ERROR $$ REFERENCE, 16 $^ IllegPageRange, 3, SEV_WARNING There are many classes of problems that can give this error message, some of which are really warnings to have a human take a closer look. $^ UnkRefRcToken, 4, SEV_WARNING There are a limited number of valid Swiss-Prot Reference Comment (RC line) tokens. This one is not one. $^ UnkRefSubType, 5, SEV_WARNING Illegal Swiss-prot Reference SubType. $^ IllegalFormat, 6, SEV_WARNING $^ IllegalAuthorName, 7, SEV_WARNING $^ YearEquZero, 8, SEV_WARNING $^ IllegalDate, 9, SEV_WARNING $^ Patent, 10, SEV_WARNING $^ Thesis, 12, SEV_WARNING $^ Book, 14, SEV_WARNING $^ DirectSubmission, 15, SEV_WARNING $^ Illegalreference, 16, SEV_ERROR $^ Fail_to_parse, 17 $^ No_references, 18, SEV_ERROR $^ Xtratext, 19, SEV_WARNING $^ InvalidInPress, 22, SEV_WARNING $^ EtAlInAuthors, 24, SEV_WARNING $^ NonDigitInPages, 25, SEV_WARNING $^ LargePageRange, 26, SEV_WARNING Total pages more than .... means that the total number in the article is greater than normal. This is usually caused by a typographical error. $^ InvertPageRange, 27, SEV_WARNING Page number may invert . . . it looks like the first page is greater that the last page. $^ SingleTokenPageRange, 28, SEV_WARNING $^ MissingBookPages, 29, SEV_WARNING $^ MissingBookAuthors, 30, SEV_WARNING $^ DateCheck, 31, SEV_WARNING $^ GsdbRefDropped, 32, SEV_WARNING $^ UnusualBookFormat, 33, SEV_WARNING $$ FEATURE, 17 $^ MultFocusedFeats, 1, SEV_ERROR $^ ExpectEmptyComment, 6, SEV_WARNING specific Swiss-Prot message for INIT_MET feature $^ DiscardData, 7, SEV_WARNING includes unbalance double quote $^ InValidEndPoint, 9, SEV_WARNING $^ MissManQual, 10, SEV_WARNING $^ NoFeatData, 11, SEV_WARNING $^ NoFragment, 12, SEV_WARNING $^ NotSeqEndPoint, 13, SEV_WARNING $^ OldNonExp, 15, SEV_WARNING $^ PartialNoNonTer, 16, SEV_WARNING $^ Pos, 17, SEV_WARNING $^ TooManyInitMet, 20, SEV_WARNING specific Swiss-Prot error message $^ UnEqualEndPoint, 22, SEV_WARNING $^ UnknownFeatKey, 23, SEV_WARNING $^ UnknownQualSpelling, 24, SEV_WARNING $^ LocationParsing, 30, SEV_ERROR $^ FeatureKeyReplaced, 32, SEV_WARNING $^ Dropped, 33, SEV_ERROR $^ UnknownDBName, 36, SEV_WARNING $^ Duplicated, 37, SEV_WARNING $^ NoSource, 38, SEV_WARNING $^ MultipleSource, 39, SEV_WARNING $$ LOCATION, 18 $^ FailedCheck, 1, SEV_WARNING $^ MixedStrand, 2, SEV_WARNING $$ GENENAME, 19 $^ IllegalGeneName, 1, SEV_WARNING $^ DELineGeneName, 2, SEV_WARNING $$ BIOSEQSETCLASS, 20 $^ NewClass, 1, SEV_INFO $$ CDREGION, 21 $^ FrameNotSet, 1, SEV_WARNING $^ InternalStopCodonFound, 2, SEV_WARNING $^ NoProteinSeq, 6, SEV_WARNING $^ TerminalStopCodonMissing, 7, SEV_WARNING $^ TranslationDiff, 8, SEV_WARNING $^ TranslationsAgree, 9, SEV_INFO $^ IllegalStart, 10, SEV_WARNING This error is caused by the start of translation being an unrecognized initiation codon when the CDS is not recognized as partial. Usually, one adds '<' or '>' on the locations to accurately reflect the biology and remove this error. On rare occasions, a /partial should be added. $^ GeneticCodeDiff, 11, SEV_WARNING Genetic code returned by Taxonomy server is different from /transl_table $^ UnevenLocation, 12, SEV_WARNING $^ ShortProtein, 13, SEV_WARNING $^ GeneticCodeAssumed, 14, SEV_WARNING $^ NoTranslationCompare, 15, SEV_WARNING $^ TranslationAdded, 16, SEV_INFO $^ InvalidGcodeTable, 17, SEV_WARNING $^ ConvertToImpFeat, 18, SEV_ERROR $^ BadLocForTranslation, 19, SEV_ERROR $^ LocationLength, 20, SEV_WARNING $^ TranslationOverride, 21, SEV_WARNING $^ FoundBadPIDType, 22, SEV_ERROR $^ FoundBadPIDNumber, 23, SEV_RROR $^ InvalidDb_xref, 24, SEV_ERROR $^ TooManyDbxref, 25, SEV_ERROR $^ Multiple_PID, 28, SEV_WARNING $$ GENEREF, 22 $^ GeneIntervalOverlap, 1, SEV_WARNING $^ NoUniqMaploc, 2, SEV_WARNING $$ PROTREF, 23 $^ NoNameForProtein, 1, SEV_WARNING $$ SEQID, 24 $^ NoSeqId, 1, SEV_ERROR $$ SERVER, 26 $^ NotUsed, 1, SEV_WARNING No protein translation sequence or organism name has been checked; Could not guess the genetic code, standard code used. $^ Failed, 2, SEV_ERROR Call for Taxonomy or/and Medline service failed. $^ GcFromSuppliedLineage, 6, SEV_WARNING $^ TaxNameWasFound, 7, SEV_INFO $$ NCBI_GI, 27 $^ BadDataFormat, 1, SEV_ERROR $$ SPROT, 28 $^ DRLine, 1, SEV_WARNING