Provided by: libbio-perl-perl_1.7.2-2_all bug


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


           # 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);

           # 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

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


       Inherits functions for managing dbm files from, 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:

          # make the index

          # here is where the retrieval key is specified
          sub get_id {
             my $line = shift;
             $line =~ /^>.+gi\|(\d+)/;


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AUTHOR - James Gilbert

       Email -


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

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

         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    :

         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

         Title   : default_id_parser
         Usage   : $id = default_id_parser( $header )
         Function: The default Fasta ID parser for
                   Returns $1 from applying the regexp /^>\s*(\S+)/
                   to $header.
         Returns : ID string
         Args    : a fasta header line string