|   | featcopy | 
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| % featcopy Read and write 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
| 
Read and write a feature table
Version: EMBOSS:6.6.0.0
   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
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -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)
   -fcircular1         boolean    Circular sequence features
   "-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
 | 
| Qualifier | Type | Description | Allowed values | Default | 
|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||
| [-features] (Parameter 1) | features | (no help text) features value | Readable feature table | Required | 
| [-outfeat] (Parameter 2) | featout | Output features UFO | Writeable feature table | unknown.gff | 
| Additional (Optional) qualifiers | ||||
| (none) | ||||
| Advanced (Unprompted) qualifiers | ||||
| (none) | ||||
| Associated qualifiers | ||||
| "-features" associated features qualifiers | ||||
| -fformat1 -fformat_features | string | Features format | Any string | |
| -iquery1 -iquery_features | string | Input query fields or ID list | Any string | |
| -ioffset1 -ioffset_features | integer | Input start position offset | Any integer value | 0 | 
| -fopenfile1 -fopenfile_features | string | Features file name | Any string | |
| -fask1 -fask_features | boolean | Prompt for begin/end/reverse | Boolean value Yes/No | N | 
| -fbegin1 -fbegin_features | integer | Start of the features to be used | Any integer value | 0 | 
| -fend1 -fend_features | integer | End of the features to be used | Any integer value | 0 | 
| -freverse1 -freverse_features | boolean | Reverse (if DNA) | Boolean value Yes/No | N | 
| -fcircular1 -fcircular_features | boolean | Circular sequence features | Boolean value Yes/No | N | 
| "-outfeat" associated featout qualifiers | ||||
| -offormat2 -offormat_outfeat | string | Output feature format | Any string | |
| -ofopenfile2 -ofopenfile_outfeat | string | Features file name | Any string | |
| -ofextension2 -ofextension_outfeat | string | File name extension | Any string | |
| -ofdirectory2 -ofdirectory_outfeat | string | Output directory | Any string | |
| -ofname2 -ofname_outfeat | string | Base file name | Any string | |
| -ofsingle2 -ofsingle_outfeat | boolean | Separate file for each entry | Boolean value Yes/No | N | 
| General qualifiers | ||||
| -auto | boolean | Turn off prompts | Boolean value Yes/No | N | 
| -stdout | boolean | Write first file to standard output | Boolean value Yes/No | N | 
| -filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N | 
| -options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N | 
| -debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N | 
| -verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y | 
| -help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N | 
| -warning | boolean | Report warnings | Boolean value Yes/No | Y | 
| -error | boolean | Report errors | Boolean value Yes/No | Y | 
| -fatal | boolean | Report fatal errors | Boolean value Yes/No | Y | 
| -die | boolean | Report dying program messages | Boolean value Yes/No | Y | 
| -version | boolean | Report version number and exit | Boolean value Yes/No | N | 
| ##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=X13776.1;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;transl_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=UniProtKB/Swiss-Prot:P10932;protein_id=CAA32023.1;translation=MSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFDVPVDVVFTSIFQNGHHDEIAALLAAGTPRTTLVALVEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQDRIAGQARINQAKVLLMQRHGWDEREAHQHLSREAMKRREPILKIAQELLGNEPSA X13776 EMBL CDS 135 1292 . + 0 ID=X13776.3;transl_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=UniProtKB/Swiss-Prot:P27017;protein_id=CAA32024.1;translation=MGSHQERPLIGLLFSETGVTADIERSHAYGALLAVEQLNREGGVGGRPIETLSQDPGGDPDRYRLCAEDFIRNRGVRFLVGCYMSHTRKAVMPVVERADALLCYPTPYEGFEYSPNIVYGGPAPNQNSAPLAAYLIRHYGERVVFIGSDYIYPRESNHVMRHLYRQHGGTVLEEIYIPLYPSDDDLQRAVERIYQARADVVFSTVVGTGTAELYRAIARRYGDGRRPPIASLTTSEAEVAKMESDVAEGQVVVAPYFSSIDTPASRAFVQACHGFFPENATITAWAEAAYWQTLLLGRAAQAAGNWRVEDVQRHLYDIDIDAPQGPVRVERQNNHSRLSSRIAEIDARGVFQVRWQSPEPIRPDPYVVVHNLDDWSASMGGGPLP X13776 EMBL promoter 8 24 . + . ID=X13776.4;note=proposed rpoN-dependent promoter X13776 EMBL promoter 65 81 . + . ID=X13776.5;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 constitutive 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 constitutive expression of amiE X13776 EMBL sequence_conflict 1281 1281 . + . ID=X13776.10;replace=g;citation=[3] | 
| ##gff-version 3 ##sequence-region X13776 1 2167 #!Date 2013-07-15 #!Type DNA #!Source-version EMBOSS 6.6.0.0 X13776 EMBL databank_entry 1 2167 . + . ID=X13776.1;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;transl_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=UniProtKB/Swiss-Prot:P10932;protein_id=CAA32023.1;translation=MSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFDVPVDVVFTSIFQNGHHDEIAALLAAGTPRTTLVALVEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQDRIAGQARINQAKVLLMQRHGWDEREAHQHLSREAMKRREPILKIAQELLGNEPSA X13776 EMBL CDS 135 1292 . + 0 ID=X13776.3;transl_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=UniProtKB/Swiss-Prot:P27017;protein_id=CAA32024.1;translation=MGSHQERPLIGLLFSETGVTADIERSHAYGALLAVEQLNREGGVGGRPIETLSQDPGGDPDRYRLCAEDFIRNRGVRFLVGCYMSHTRKAVMPVVERADALLCYPTPYEGFEYSPNIVYGGPAPNQNSAPLAAYLIRHYGERVVFIGSDYIYPRESNHVMRHLYRQHGGTVLEEIYIPLYPSDDDLQRAVERIYQARADVVFSTVVGTGTAELYRAIARRYGDGRRPPIASLTTSEAEVAKMESDVAEGQVVVAPYFSSIDTPASRAFVQACHGFFPENATITAWAEAAYWQTLLLGRAAQAAGNWRVEDVQRHLYDIDIDAPQGPVRVERQNNHSRLSSRIAEIDARGVFQVRWQSPEPIRPDPYVVVHNLDDWSASMGGGPLP X13776 EMBL promoter 8 24 . + . ID=X13776.4;note=proposed rpoN-dependent promoter X13776 EMBL promoter 65 81 . + . ID=X13776.5;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 constitutive 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 constitutive expression of amiE X13776 EMBL sequence_conflict 1281 1281 . + . ID=X13776.10;replace=g;citation=[3] | 
| Program name | Description | 
|---|---|
| aligncopy | Read and write alignments | 
| aligncopypair | Read and write pairs from alignments | 
| biosed | Replace or delete sequence sections | 
| codcopy | Copy and reformat a codon usage table | 
| cutseq | Remove a section from a sequence | 
| degapseq | Remove non-alphabetic (e.g. gap) characters from sequences | 
| descseq | Alter the name or description of a sequence | 
| entret | Retrieve 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 | 
| featmerge | Merge two overlapping feature tables | 
| featreport | Read and write 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 | Mask all ambiguity characters in nucleotide sequences with N | 
| maskambigprot | Mask 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 | Read and write (return) one set of sequences from many | 
| pasteseq | Insert one sequence into another | 
| revseq | Reverse and complement a nucleotide sequence | 
| seqcount | Read and count sequences | 
| seqret | Read and write (return) sequences | 
| seqretsetall | Read and write (return) many sets of sequences | 
| seqretsplit | Read sequences and write them to individual files | 
| sizeseq | Sort sequences by size | 
| skipredundant | Remove redundant sequences from an input set | 
| skipseq | Read and write (return) 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 | Remove vectors from the ends of nucleotide sequence(s) | 
| yank | Add a sequence reference (a full USA) to a list file | 
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.