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Bio::Index::SwissPfam(User Contributed Perl DocumentatBio::Index::SwissPfam(3)

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.

	 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://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

perl v5.32.0			  2019-12-07	      Bio::Index::SwissPfam(3)

NAME | SYNOPSIS | DESCRIPTION | FEED_BACK | AUTHOR - Ewan Birney | APPENDIX

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