/ 
FAST-1.06
River stage zero No dependents
/ FAST::Bio::SeqIO::interpro

NAME

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

SYNOPSIS

# do not call this module directly, use FAST::Bio::SeqIO

use strict;
use FAST::Bio::SeqIO;

my $io = FAST::Bio::SeqIO->new(-format => "interpro",
                         -file   => $interpro_file);

while (my $seq = $io->next_seq) {
  # use the Sequence object
}

DESCRIPTION

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

FAST::Bio::SeqIO::interpro will also attach the annotation given in the XML file to the FAST::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:

https://redmine.open-bio.org/projects/bioperl/

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 FAST::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    :