Bio::SeqIO::interpro.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::SeqIO::interpro - InterProScan XML input/output stream

SYNOPSIS

   # do not call this module directly, use Bio::SeqIO
 
   use strict;
   use Bio::SeqIO;
 
   my $io = Bio::SeqIO->new(-format => "interpro",
                            -file   => $interpro_file);
 
   while (my $seq = $io->next_seq) {
     # use the Sequence object
   }
 
 

DESCRIPTION

Bio::SeqIO::interpro will parse Interpro scan XML (version 1.2) and create Bio::SeqFeature::Generic objects based on the contents of the XML document.

Bio::SeqIO::interpro will also attach the annotation given in the XML file to the Bio::SeqFeature::Generic objects that it creates.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.
   bioperl-l@bioperl.org                  - General discussion
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 
 

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:
   http://bugzilla.open-bio.org/
 
 

AUTHOR - Jared Fox

Email jaredfox@ucla.edu

CONTRIBUTORS

Allen Day allenday@ucla.edu

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

next_seq

  Title   : next_seq
  Usage   : my $seqobj = $stream->next_seq
  Function: Retrieves the next sequence from a SeqIO::interpro stream.
  Returns : A Bio::Seq::RichSeq object
  Args    :
 
 

_initialize

  Title   : _initialize
  Usage   : 
  Function: 
  Returns :
  Args    :
 
 

_sequence_factory

  Title   : _sequence_factory
  Usage   : 
  Function: 
  Returns :
  Args    :
 
 

_xml_parser

  Title   : _xml_parser
  Usage   : 
  Function: 
  Returns :
  Args    :
 
 

_parse_xml

  Title   : _parse_xml
  Usage   : 
  Function: 
  Returns :
  Args    :
 
 

_dom

  Title   : _dom
  Usage   : 
  Function: 
  Returns :
  Args    :