featcopy

 

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Function

Read and write 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 
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:6.5.0.0

   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 2012-07-15
#!Type DNA
#!Source-version EMBOSS 6.5.0.0
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 Rice
European 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.

History

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments

None