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:
https://github.com/bioperl/bioperl-live/issues
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 :