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featcopy |
Wiki
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Function
Read and write a feature tableDescription
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 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
Command line arguments
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 |
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=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] |
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 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] |
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 | 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 |
Author(s)
Peter RiceEuropean Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.