| Bio::SeqIO::interpro(3pm) | User Contributed Perl Documentation | Bio::SeqIO::interpro(3pm) |
Bio::SeqIO::interpro - InterProScan XML input/output stream
# 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
}
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.
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
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.
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
Email jaredfox@ucla.edu
Allen Day allenday@ucla.edu
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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 :
Title : _initialize Usage : Function: Returns : Args :
Title : _sequence_factory Usage : Function: Returns : Args :
Title : _xml_parser Usage : Function: Returns : Args :
Title : _parse_xml Usage : Function: Returns : Args :
Title : _dom Usage : Function: Returns : Args :
| 2018-10-27 | perl v5.26.2 |