Provided by: libbio-perl-perl_1.6.901-2_all bug

NAME

       Bio::Index::EMBL - Interface for indexing (multiple) EMBL/Swissprot .dat files (i.e. flat
       file EMBL/Swissprot format).

SYNOPSIS

           # Complete code for making an index for several
           # EMBL files
           use Bio::Index::EMBL;
           use strict;

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

           # Print out several sequences present in the index
           # in Fasta format
           use Bio::Index::EMBL;
           use strict;

           my $Index_File_Name = shift;
           my $inx = Bio::Index::EMBL->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);
           }

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

DESCRIPTION

       Inherits functions for managing dbm files from Bio::Index::Abstract.pm, and provides the
       basic funtionallity for indexing EMBL files, and retrieving the sequence from them.
       Heavily snaffled from James Gilbert and his Fasta system. Note: for best results 'use
       strict'.

       The keys are the identifiers in the ID and AC lines.

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@sanger.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: Specialist function to index EMBL format files.
                   Is provided with a filename and an integer
                   by make_index in its SUPER class.
         Example :
         Returns :
         Args    :

   _file_format
        Title   : _file_format
        Usage   : Internal function for indexing system
        Function: Provides file format for this database
        Example :
        Returns :
        Args    :