Bio::Index::SwissPfam

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

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list: [email protected] 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://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 _

_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