                                  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:6.5.6.0

   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


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 2012-07-15
#!Type DNA
#!Source-version EMBOSS 6.5.6.0
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        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 (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
