Bio::Index::GenBank(3pm)				User Contributed Perl Documentation				  Bio::Index::GenBank(3pm)

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://redmine.open-bio.org/projects/bioperl/

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 v5.14.2							    2012-03-02						  Bio::Index::GenBank(3pm)