focal (3) Bio::SeqIO::interpro.3pm.gz

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    :