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Bio::Index::GenBank(3)User Contributed Perl DocumentatioBio::Index::GenBank(3)

NAME
       Bio::Index::GenBank - Interface for indexing one	or more	GenBank	files
       (i.e. flat file GenBank format).

SYNOPSIS
	   # Complete code for making an index for one or more GenBank files
	   use strict;
	   use Bio::Index::GenBank;

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

	   # Print out sequences present in the	index in gcg format
	   use Bio::Index::GenBank;
	   use Bio::SeqIO;
	   use strict;

	   my $Index_File_Name = shift;
	   my $inx = Bio::Index::GenBank->new(-filename	=> $Index_File_Name);
	   my $seqio = Bio::SeqIO->new(-format => 'gcg');
	   foreach my $id (@ARGV) {
	       my $seq = $inx->fetch($id); # Returns Bio::Seq object
	       $seqio->write_seq($seq);
	   }

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

DESCRIPTION
       By default the index that is created uses the LOCUS, ACCESSION, and
       VERSION identifiers as keys. Inherits functions for managing dbm	files
       from Bio::Index::Abstract.pm, and provides the basic functionality for
       indexing	GenBank	files, and retrieving the sequence 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
	  $inx->make_index($file_name);

	  # here is where the retrieval	key is specified
	  sub get_id {
	     my	$line =	shift;
	     $line =~ /clone="(\S+)"/;
	     $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
       Email - birney@ebi.ac.uk

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: Specialized function	to index GenBank 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 : reference 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 GenBank.pm
	 Returns : Array of specified ids
	 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::GenBank(3)

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

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