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

NAME

       Bio::Index::Fasta - Interface for indexing (multiple) fasta files

SYNOPSIS

	   # Make an index for one or more fasta files
	   use Bio::Index::Fasta;
	   use strict;

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

	   # Once the index is made it can accessed, either in the
	   # same script or a different one
	   use Bio::Index::Fasta;
	   use strict;

	   my $Index_File_Name = shift;
	   my $inx = Bio::Index::Fasta->new(-filename => $Index_File_Name);
	   my $out = Bio::SeqIO->new(-format => 'Fasta',
				     -fh => *STDOUT);

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

	   # or, alternatively
	   my $id;
	   my $seq = $inx->get_Seq_by_id($id); # identical to fetch()

DESCRIPTION

       Inherits functions for managing dbm files from Bio::Index::Abstract.pm, and provides the basic funtionallity for indexing fasta files, and
       retrieving the sequence from them. For best results 'use strict'.

       Bio::Index::Fasta supports the Bio::DB::BioSeqI interface, meaning it can be used as a Sequence database for other parts of bioperl

       Additional example code is available in scripts/index/*PLS and in the Bioperl Tutorial (<http://www.bioperl.org/wiki/Bptutorial.pl>)

       Note that by default the key for the sequence will be the first continuous string after the '>' in the fasta header. If you want to use a
       specific substring of the fasta header you must use the id_parser() method.

       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 =~ /^>.+gi|(d+)/;
	     $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 - James Gilbert
       Email - jgrg@sanger.ac.uk

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

   _file_format
	Title	: _file_format
	Function: The file format for this package, which is needed
		  by the SeqIO system when reading the sequence.
	Returns : 'Fasta'

   _index_file
	 Title	 : _index_file
	 Usage	 : $index->_index_file( $file_name, $i )
	 Function: Specialist function to index FASTA 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.  Useful
		   for (for instance) specifying a different
		   parser for different flavours of FASTA file.
		   Returns &default_id_parser (see below) if not
		   set. If you supply your own id_parser
		   subroutine, then it should expect a fasta
		   description line.  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( $header )
	 Function: The default Fasta ID parser for Fasta.pm
		   Returns $1 from applying the regexp /^>s*(S+)/
		   to $header.
	 Returns : ID string
	 Args	 : a fasta header line string

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