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 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'.

FEED_BACK¶

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

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

AUTHOR - Ewan Birney¶

APPENDIX¶

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