Bio::Index::EMBL(3) Interface for indexing (multiple) EMBL/Swissprot


# 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 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.


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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    :