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

NAME
       Bio::Index::Swissprot - Interface for indexing one or more Swissprot
       files.

SYNOPSIS
	 # Make	an index for one or more Swissprot files:

	   use Bio::Index::Swissprot;
	   use strict;

	   my $index_file_name = shift;
	   my $inx = Bio::Index::Swissprot->new(
	       -filename => $index_file_name,
	       -write_flag => 1);
	   $inx->make_index(@ARGV);

	 # Print out several sequences present in the index in Genbank
	 # format:

	   use Bio::Index::Swissprot;
	   use Bio::SeqIO;
	   use strict;

	   my $out = Bio::SeqIO->new( -format => 'genbank',
				      -fh => \*STDOUT );
	   my $index_file_name = shift;
	   my $inx = Bio::Index::Swissprot->new(-filename => $index_file_name);

	   foreach my $id (@ARGV) {
	       my $seq = $inx->fetch($id); # Returns a Bio::Seq	object
	       $out->write_seq($seq);
	   }

	   # alternatively
	   my ($id, $acc);
	   my $seq1 = $inx->get_Seq_by_id($id);
	   my $seq2 = $inx->get_Seq_by_acc($acc);

DESCRIPTION
       By default the index that is created uses the AC	and ID identifiers as
       keys. This module inherits functions for	managing dbm files from
       Bio::Index::Abstract.pm,	and provides the basic functionality for
       indexing	Swissprot files	and retrieving Sequence	objects	from them. For
       best results 'use strict'.

       You can also set	or customize the unique	key used to retrieve by
       writing your own	function and calling the id_parser() method.  For
       example:

	  $inx->id_parser(\&get_id);
	  # make the index
	  $inx->make_index($index_file_name);

	  # here is where the retrieval	key is specified
	  sub get_id {
	     my	$line =	shift;
	     $line =~ /^KW\s+([A-Z]+)/i;
	     $1;
	  }

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
       Also lorenz@ist.org, bosborne at	alum.mit.edu

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	Swissprot format files.
		   Is provided with a filename and an integer
		   by make_index in its	SUPER class.
	 Example :
	 Returns :
	 Args	 :

   id_parser
	 Title	 : id_parser
	 Usage	 : $index->id_parser( CODE )
	 Function: Stores or returns the code used by record_id	to
		   parse the ID	for record from	a string.
		   Returns \&default_id_parser (see below) if not
		   set.	An entry will be added to
		   the index for each string in	the list returned.
	 Example : $index->id_parser( \&my_id_parser )
	 Returns : ref to CODE if called without arguments
	 Args	 : CODE

   default_id_parser
	 Title	 : default_id_parser
	 Usage	 : $id = default_id_parser( $line )
	 Function: The default parser for Swissprot.pm
		   Returns $1 from applying the	regexp /^ID\s*(\S+)/
		   or /^AC\s+([A-Z0-9]+)/ to the current line.
	 Returns : ID string
	 Args	 : a line string

   _file_format
	Title	: _file_format
	Usage	: Internal function for	indexing system
	Function: Provides file	format for this	database
	Example	:
	Returns	:
	Args	:

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

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

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