Provided by: libbio-perl-perl_1.7.6-3_all bug


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


           # 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');

           # 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

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


       Inherits functions for managing dbm files from, and provides the
       basic funtionality 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.


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AUTHOR - Ewan Birney

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

         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    :

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