Provided by: libbio-perl-perl_1.6.901-2_all bug

NAME

       Bio::Index::SwissPfam - Interface for indexing swisspfam files

SYNOPSIS

           use Bio::Index::SwissPfam;
           use strict;

           my $Index_File_Name = shift;
           my $inx = Bio::Index::SwissPfam->new('-filename' => $Index_File_Name,
                                                '-write_flag' => 'WRITE');
           $inx->make_index(@ARGV);

           use Bio::Index::SwissPfam;
           use strict;

           my $Index_File_Name = shift;
           my $inx = Bio::Index::SwissPfam->new('-filename' => $Index_File_Name);

           foreach my $id (@ARGV) {
               my $seq = $inx->fetch($id); # Returns stream
                    while( <$seq> ) {
                        if(/^>/) {
                              print;
                                 last;
                        }
                    }
           }

DESCRIPTION

       SwissPfam is one of the flat files released with Pfam. This modules provides a way of
       indexing this module.

       Inherits functions for managing dbm files from Bio::Index::Abstract.pm, and provides the
       basic funtionallity for indexing SwissPfam files.  Only retrieves FileStreams at the
       moment. Once we have something better (ie, an object!), will use that. Heavily snaffled
       from Index::Fasta system of James Gilbert. Note: for best results 'use strict'.

FEED_BACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to one of the Bioperl mailing lists.  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 the bugs and their
       resolution.  Bug reports can be submitted via the web:

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

AUTHOR - Ewan Birney

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are
       usually preceded with a _

   _index_file
         Title   : _index_file
         Usage   : $index->_index_file( $file_name, $i )
         Function: Specialist function to index swisspfam format files.
                   Is provided with a filename and an integer
                   by make_index in its SUPER class.
         Example :
         Returns :
         Args    :

   fetch
         Title   : fetch
         Usage   : $index->fetch( $id )
         Function: Returns a Bio::Seq object from the index
         Example : $seq = $index->fetch( 'dJ67B12' )
         Returns : Bio::Seq object
         Args    : ID