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/.

       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://github.com/bioperl/bioperl-live/issues

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