Bio::Index EMBL
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Bio::Index::EMBL - Interface for indexing (multiple) EMBL/Swissprot
.dat files (ie flat file embl/swissprot format).
Package variables
No package variables defined.
Included modules
    # 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 $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's
Fasta system. Note: for best results 'use strict'.
No description
No description
Methods description
_file_formatcode    nextTop
 Title   : _file_format
Usage : Internal function for indexing system
Function: Provides file format for this database
Example :
Returns :
Args :
  Title   : _index_file
Usage : $index->_index_file( $file_name, $i )
Function: Specialist function to index EMBL format files.
Is provided with a filename and an integer
by make_index in its SUPER class.
Example :
Returns :
Args :
Methods code
sub _file_format {
   my ($self,@args) = @_;

   return 'EMBL';

sub _index_file {
    my( $self,
        $file, # File name
$i # Index-number of file being indexed
) = @_; my( $begin, # Offset from start of file of the start
# of the last found record.
$id, # ID of last found record.
@accs, # accession of last record. Also put into the index
); $begin = 0; open EMBL, $file or $self->throw("Can't open file for read : $file"); # Main indexing loop
$id = undef; @accs = (); while (<EMBL>) { if( /^\/\// ) { if( ! defined $id ) { $self->throw("Got to a end of entry line for an EMBL flat file with no parsed ID. Considering this a problem!"); next; } if( ! @accs ) { $self->warn("For id [$id] in embl flat file, got no accession number. Storing id index anyway"); } $self->add_record($id, $i, $begin); foreach my $acc (@accs) { if( $acc ne $id ) { $self->add_record($acc, $i, $begin); } } } elsif (/^ID\s+(\S+)/) { $id = $1; # not sure if I like this. Assummes tell is in bytes.
# we could tell before each line and save it.
$begin = tell(EMBL) - length( $_ ); } elsif (/^AC\s+(.*)?/) { push @accs , split (/[; ]+/, $1); } else { # do nothing
} } close EMBL; return 1;
sub _type_stamp {
    return '__EMBL_FLAT__'; # What kind of index are we?
} #
# Suggested fix by Michael G Schwern <> to
# get around a clash with CPAN shell...
sub _version {
    return $VERSION;
General documentation
Mailing ListsTop
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.             - General discussion - About the mailing lists
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via
email or the web:
AUTHOR - Ewan BirneyTop
Email -
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _