featcopy

 

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 features: paamir.gff3
Features output [paamir.gff]: 

Go to the input files for this example
Go to the output files for this example

Command line arguments

   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. 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

Standard (Mandatory) qualifiers Allowed values Default
[-features]
(Parameter 1)
(no help text) features value Readable feature table Required
[-outfeat]
(Parameter 2)
Output features UFO Writeable feature table unknown.gff
Additional (Optional) qualifiers Allowed values Default
(none)
Advanced (Unprompted) qualifiers Allowed values Default
(none)

Input file format

featcopy reads any normal features UFOs.

Input files for usage example

File: paamir.gff3

##gff-version 3
##sequence-region PAAMIR 1 2167
#!Date 2008-07-11
#!Type DNA
#!Source-version EMBOSS 6.0.0
PAAMIR	EMBL	databank_entry	1	2167	0.000	+	.	ID="PAAMIR.1";db_xref="taxon:287";organism="Pseudomonas aeruginosa";strain="PAC";isolate="PAC 1";map="38 min"
PAAMIR	EMBL	CDS	1289	1879	0.000	+	0	ID="PAAMIR.2";db_xref="SWISS-PROT:P10932";note="aliphatic amidase regulator, positive regulator of amiE";transl_table=11;gene="amiR";protein_id="CAA32023.1";translation="MSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFDVPVDVVFTSIFQNGHHDEIAALLAAGTPRTTLVALVEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQDRIAGQARINQAKVLLMQRHGWDEREAHQHLSREAMKRREPILKIAQELLGNEPSA"
PAAMIR	EMBL	CDS	135	1292	0.000	+	0	ID="PAAMIR.3";db_xref="SWISS-PROT:P27017";note="negative regulator of amiR";transl_table=11;gene="amiC";protein_id="CAA32024.1";translation="MGSHQERPLIGLLFSETGVTADIERSHAYGALLAVEQLNREGGVGGRPIETLSQDPGGDPDRYRLCAEDFIRNRGVRFLVGCYMSHTRKAVMPVVERADALLCYPTPYEGFEYSPNIVYGGPAPNQNSAPLAAYLIRHYGERVVFIGSDYIYPRESNHVMRHLYRQHGGTVLEEIYIPLYPSDDDLQRAVERIYQARADVVFSTVVGTGTAELYRAIARRYGDGRRPPIASLTTSEAEVAKMESDVAEGQVVVAPYFSSIDTPASRAFVQACHGFFPENATITAWAEAAYWQTLLLGRAAQAAGNWRVEDVQRHLYDIDIDAPQGPVRVERQNNHSRLSSRIAEIDARGVFQVRWQSPEPIRPDPYVVVHNLDDWSASMGGGPLP"
PAAMIR	EMBL	promoter	8	24	0.000	+	.	ID="PAAMIR.4";note="proposed rpoN-dependent promoter"
PAAMIR	EMBL	promoter	65	81	0.000	+	.	ID="PAAMIR.5";note="proposed rpoN-dependent promoter"
PAAMIR	EMBL	ribosome_entry_site	121	126	0.000	+	.	ID="PAAMIR.6";note="proposed Shine-Dalgarno sequence"
PAAMIR	EMBL	sequence_variant	912	1167	0.000	+	.	ID="PAAMIR.7";note="ClaI fragment deleted in pSW36, constitutive phenotype";replace="";gene="amiC"
PAAMIR	EMBL	located_sequence_feature	1	1	0.000	+	.	ID="PAAMIR.8";featflags="0x40";note="last base of an XhoI site"
PAAMIR	EMBL	located_sequence_feature	648	653	0.000	+	.	ID="PAAMIR.9";note="end of 658bp XhoI fragment, deletion in pSW3 causes constitutive expression of amiE"
PAAMIR	EMBL	misc_difference	1281	1281	0.000	+	.	ID="PAAMIR.10";featflags="0x40";replace="g";citation=[3]

Output file format

featcopy outputs a feature file.

Output files for usage example

File: paamir.gff

##gff-version 3
##sequence-region PAAMIR 1 2167
#!Date 2008-07-15
#!Type DNA
#!Source-version EMBOSS 6.0.0
PAAMIR	EMBL	databank_entry	1	2167	0.000	+	.	ID="PAAMIR.1";db_xref="taxon:287";organism="Pseudomonas aeruginosa";strain="PAC";isolate="PAC 1";map="38 min"
PAAMIR	EMBL	CDS	1289	1879	0.000	+	0	ID="PAAMIR.2";db_xref="SWISS-PROT:P10932";note="aliphatic amidase regulator, positive regulator of amiE";transl_table=11;gene="amiR";protein_id="CAA32023.1";translation="MSANSLLGSLRELQVLVLNPPGEVSDALVLQLIRIGCSVRQCWPPPEAFDVPVDVVFTSIFQNGHHDEIAALLAAGTPRTTLVALVEYESPAVLSQIIELECHGVITQPLDAHRVLPVLVSARRISEEMAKLKQKTEQLQDRIAGQARINQAKVLLMQRHGWDEREAHQHLSREAMKRREPILKIAQELLGNEPSA"
PAAMIR	EMBL	CDS	135	1292	0.000	+	0	ID="PAAMIR.3";db_xref="SWISS-PROT:P27017";note="negative regulator of amiR";transl_table=11;gene="amiC";protein_id="CAA32024.1";translation="MGSHQERPLIGLLFSETGVTADIERSHAYGALLAVEQLNREGGVGGRPIETLSQDPGGDPDRYRLCAEDFIRNRGVRFLVGCYMSHTRKAVMPVVERADALLCYPTPYEGFEYSPNIVYGGPAPNQNSAPLAAYLIRHYGERVVFIGSDYIYPRESNHVMRHLYRQHGGTVLEEIYIPLYPSDDDLQRAVERIYQARADVVFSTVVGTGTAELYRAIARRYGDGRRPPIASLTTSEAEVAKMESDVAEGQVVVAPYFSSIDTPASRAFVQACHGFFPENATITAWAEAAYWQTLLLGRAAQAAGNWRVEDVQRHLYDIDIDAPQGPVRVERQNNHSRLSSRIAEIDARGVFQVRWQSPEPIRPDPYVVVHNLDDWSASMGGGPLP"
PAAMIR	EMBL	promoter	8	24	0.000	+	.	ID="PAAMIR.4";note="proposed rpoN-dependent promoter"
PAAMIR	EMBL	promoter	65	81	0.000	+	.	ID="PAAMIR.5";note="proposed rpoN-dependent promoter"
PAAMIR	EMBL	ribosome_entry_site	121	126	0.000	+	.	ID="PAAMIR.6";note="proposed Shine-Dalgarno sequence"
PAAMIR	EMBL	sequence_variant	912	1167	0.000	+	.	ID="PAAMIR.7";note="ClaI fragment deleted in pSW36, constitutive phenotype";replace="";gene="amiC"
PAAMIR	EMBL	located_sequence_feature	1	1	0.000	+	.	ID="PAAMIR.8";featflags="0x40";note="last base of an XhoI site"
PAAMIR	EMBL	located_sequence_feature	648	653	0.000	+	.	ID="PAAMIR.9";note="end of 658bp XhoI fragment, deletion in pSW3 causes constitutive expression of amiE"
PAAMIR	EMBL	sequence_difference	1281	1281	0.000	+	.	ID="PAAMIR.10";featflags="0x40";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
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 all 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
pasteseq Insert one sequence into another
revseq Reverse and complement a nucleotide sequence
seqret Reads and writes (returns) 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
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 (pmr © ebi.ac.uk)
Informatics Division, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

History

Target users

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

Comments

None