featcopy Wiki The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki. Please help by correcting and extending the Wiki pages. Function Reads and writes a feature table Description featcopy reads a feature table and reformats it in any of the supported output feature formats. Usage Here is a sample session with featcopy % featcopy Reads and writes a feature table Input feature table: paamir.gff3 Features output [x13776.gff]: Go to the input files for this example Go to the output files for this example Command line arguments Reads and writes a feature table Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-features] features (no help text) features value [-outfeat] featout [unknown.gff] Output features UFO Additional (Optional) qualifiers: (none) Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-features" associated qualifiers -fformat1 string Features format -fopenfile1 string Features file name -fask1 boolean Prompt for begin/end/reverse -fbegin1 integer Start of the features to be used -fend1 integer End of the features to be used -freverse1 boolean Reverse (if DNA) "-outfeat" associated qualifiers -offormat2 string Output feature format -ofopenfile2 string Features file name -ofextension2 string File name extension -ofdirectory2 string Output directory -ofname2 string Base file name -ofsingle2 boolean Separate file for each entry General qualifiers: -auto boolean Turn off prompts -stdout boolean Write first file to standard output -filter boolean Read first file from standard input, write first file to standard output -options boolean Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report dying program messages -version boolean Report version number and exit Input file format featcopy reads any normal features UFOs. Input files for usage example File: paamir.gff3 ##gff-version 3 ##sequence-region X13776 1 2167 #!Date 2011-05-24 #!Type DNA #!Source-version EMBOSS 6.4.0.0 X13776 EMBL databank_entry 1 2167 . + . ID=X1377 6.1;organism=Pseudomonas aeruginosa;map=38 min;strain=PAC;isolate=PAC 1;mol_type =genomic DNA;db_xref=taxon:287 X13776 EMBL CDS 1289 1879 . + 0 ID=X13776.2;tran sl_table=11;gene=amiR;note=aliphatic amidase regulator%2C positive regulator of amiE;db_xref=GOA:P10932;db_xref=InterPro:IPR005561;db_xref=InterPro:IPR008327;db _xref=InterPro:IPR011006;db_xref=InterPro:IPR011991;db_xref=PDB:1QO0;db_xref=Uni ProtKB/Swiss-Prot:P10932;protein_id=CAA32023.1;translation=MSANSLLGSLRELQVLVLNPP GEVSDALVLQLIRIGCSVRQCWPPPEAFDVPVDVVFTSIFQNGHHDEIAALLAAGTPRTTLVALVEYESPAVLSQIIELE CHGVITQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQDRIAGQARINQAKVLLMQRHGWDEREAHQHLSREAMKRREP ILKIAQELLGNEPSA X13776 EMBL CDS 135 1292 . + 0 ID=X13776.3;tran sl_table=11;gene=amiC;note=negative regulator of amiR;db_xref=GOA:P27017;db_xref =InterPro:IPR000709;db_xref=PDB:1PEA;db_xref=PDB:1QNL;db_xref=PDB:1QO0;db_xref=U niProtKB/Swiss-Prot:P27017;protein_id=CAA32024.1;translation=MGSHQERPLIGLLFSETGV TADIERSHAYGALLAVEQLNREGGVGGRPIETLSQDPGGDPDRYRLCAEDFIRNRGVRFLVGCYMSHTRKAVMPVVERAD ALLCYPTPYEGFEYSPNIVYGGPAPNQNSAPLAAYLIRHYGERVVFIGSDYIYPRESNHVMRHLYRQHGGTVLEEIYIPL YPSDDDLQRAVERIYQARADVVFSTVVGTGTAELYRAIARRYGDGRRPPIASLTTSEAEVAKMESDVAEGQVVVAPYFSS IDTPASRAFVQACHGFFPENATITAWAEAAYWQTLLLGRAAQAAGNWRVEDVQRHLYDIDIDAPQGPVRVERQNNHSRLS SRIAEIDARGVFQVRWQSPEPIRPDPYVVVHNLDDWSASMGGGPLP X13776 EMBL promoter 8 24 . + . ID=X1377 6.4;note=proposed rpoN-dependent promoter X13776 EMBL promoter 65 81 . + . ID=X1377 6.5;note=proposed rpoN-dependent promoter X13776 EMBL ribosome_entry_site 121 126 . + . ID=X13776.6;note=proposed Shine-Dalgarno sequence X13776 EMBL sequence_variant 912 1167 . + . ID=X13776.7;gene=amiC;replace=;note=ClaI fragment deleted in pSW36%2C constituti ve phenotype X13776 EMBL sequence_feature 1 1 . + . ID=X13776.8;note=last base of an XhoI site X13776 EMBL sequence_feature 648 653 . + . ID=X13776.9;note=end of 658bp XhoI fragment%2C deletion in pSW3 causes constitut ive expression of amiE X13776 EMBL sequence_conflict 1281 1281 . + . ID=X13776.10;replace=g;citation=[3] Output file format featcopy outputs a feature file. Output files for usage example File: x13776.gff ##gff-version 3 ##sequence-region X13776 1 2167 #!Date 2011-07-15 #!Type DNA #!Source-version EMBOSS 6.4.0.0 X13776 EMBL databank_entry 1 2167 . + . ID=X1377 6.1;organism=Pseudomonas aeruginosa;map=38 min;strain=PAC;isolate=PAC 1;mol_type =genomic DNA;db_xref=taxon:287 X13776 EMBL CDS 1289 1879 . + 0 ID=X13776.2;tran sl_table=11;gene=amiR;note=aliphatic amidase regulator%2C positive regulator of amiE;db_xref=GOA:P10932;db_xref=InterPro:IPR005561;db_xref=InterPro:IPR008327;db _xref=InterPro:IPR011006;db_xref=InterPro:IPR011991;db_xref=PDB:1QO0;db_xref=Uni ProtKB/Swiss-Prot:P10932;protein_id=CAA32023.1;translation=MSANSLLGSLRELQVLVLNPP GEVSDALVLQLIRIGCSVRQCWPPPEAFDVPVDVVFTSIFQNGHHDEIAALLAAGTPRTTLVALVEYESPAVLSQIIELE CHGVITQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQDRIAGQARINQAKVLLMQRHGWDEREAHQHLSREAMKRREP ILKIAQELLGNEPSA X13776 EMBL CDS 135 1292 . + 0 ID=X13776.3;tran sl_table=11;gene=amiC;note=negative regulator of amiR;db_xref=GOA:P27017;db_xref =InterPro:IPR000709;db_xref=PDB:1PEA;db_xref=PDB:1QNL;db_xref=PDB:1QO0;db_xref=U niProtKB/Swiss-Prot:P27017;protein_id=CAA32024.1;translation=MGSHQERPLIGLLFSETGV TADIERSHAYGALLAVEQLNREGGVGGRPIETLSQDPGGDPDRYRLCAEDFIRNRGVRFLVGCYMSHTRKAVMPVVERAD ALLCYPTPYEGFEYSPNIVYGGPAPNQNSAPLAAYLIRHYGERVVFIGSDYIYPRESNHVMRHLYRQHGGTVLEEIYIPL YPSDDDLQRAVERIYQARADVVFSTVVGTGTAELYRAIARRYGDGRRPPIASLTTSEAEVAKMESDVAEGQVVVAPYFSS IDTPASRAFVQACHGFFPENATITAWAEAAYWQTLLLGRAAQAAGNWRVEDVQRHLYDIDIDAPQGPVRVERQNNHSRLS SRIAEIDARGVFQVRWQSPEPIRPDPYVVVHNLDDWSASMGGGPLP X13776 EMBL promoter 8 24 . + . ID=X1377 6.4;note=proposed rpoN-dependent promoter X13776 EMBL promoter 65 81 . + . ID=X1377 6.5;note=proposed rpoN-dependent promoter X13776 EMBL ribosome_entry_site 121 126 . + . ID=X13776.6;note=proposed Shine-Dalgarno sequence X13776 EMBL sequence_variant 912 1167 . + . ID=X13776.7;gene=amiC;replace=;note=ClaI fragment deleted in pSW36%2C constituti ve phenotype X13776 EMBL sequence_feature 1 1 . + . ID=X13776.8;note=last base of an XhoI site X13776 EMBL sequence_feature 648 653 . + . ID=X13776.9;note=end of 658bp XhoI fragment%2C deletion in pSW3 causes constitut ive expression of amiE X13776 EMBL sequence_conflict 1281 1281 . + . ID=X13776.10;replace=g;citation=[3] Data files None. Notes None. References None. Warnings None. Diagnostic Error Messages None. Exit status It always exits with status 0. Known bugs None. See also Program name Description aligncopy Reads and writes alignments aligncopypair Reads and writes pairs from alignments biosed Replace or delete sequence sections codcopy Copy and reformat a codon usage table cutseq Removes a section from a sequence degapseq Removes non-alphabetic (e.g. gap) characters from sequences descseq Alter the name or description of a sequence entret Retrieves sequence entries from flatfile databases and files extractalign Extract regions from a sequence alignment extractfeat Extract features from sequence(s) extractseq Extract regions from a sequence featreport Reads and writes a feature table feattext Return a feature table original text listor Write a list file of the logical OR of two sets of sequences makenucseq Create random nucleotide sequences makeprotseq Create random protein sequences maskambignuc Masks all ambiguity characters in nucleotide sequences with N maskambigprot Masks all ambiguity characters in protein sequences with X maskfeat Write a sequence with masked features maskseq Write a sequence with masked regions newseq Create a sequence file from a typed-in sequence nohtml Remove mark-up (e.g. HTML tags) from an ASCII text file noreturn Remove carriage return from ASCII files nospace Remove whitespace from an ASCII text file notab Replace tabs with spaces in an ASCII text file notseq Write to file a subset of an input stream of sequences nthseq Write to file a single sequence from an input stream of sequences nthseqset Reads and writes (returns) one set of sequences from many pasteseq Insert one sequence into another revseq Reverse and complement a nucleotide sequence seqcount Reads and counts sequences seqret Reads and writes (returns) sequences seqretsetall Reads and writes (returns) many sets of sequences seqretsplit Reads sequences and writes them to individual files sizeseq Sort sequences by size skipredundant Remove redundant sequences from an input set skipseq Reads and writes (returns) sequences, skipping first few splitsource Split sequence(s) into original source sequences splitter Split sequence(s) into smaller sequences trimest Remove poly-A tails from nucleotide sequences trimseq Remove unwanted characters from start and end of sequence(s) trimspace Remove extra whitespace from an ASCII text file union Concatenate multiple sequences into a single sequence vectorstrip Removes vectors from the ends of nucleotide sequence(s) yank Add a sequence reference (a full USA) to a list file Author(s) Peter Rice European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Please report all bugs to the EMBOSS bug team (emboss-bug (c) emboss.open-bio.org) not to the original author. History Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None