Bio::SeqIO::interpro(3User Contributed Perl DocumentatiBio::SeqIO::interpro(3)NAMEBio::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
}
DESCRIPTIONBio::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 :
perl v5.14.1 2011-07-22 Bio::SeqIO::interpro(3)