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 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.

FEED_BACK¶

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

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

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 _

  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    :