Provided by: libbio-perl-perl_1.7.7-1_all bug


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


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

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

           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(/^>/) {


       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, and provides the
       basic funtionality 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'.


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AUTHOR - Ewan Birney


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

         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    :

         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