Bio::Index EMBL
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Bio::Index::EMBL - Interface for indexing (multiple) EMBL/Swissprot
.dat files (i.e. 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 ($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.
No description
No description
Methods description
_index_filecode    nextTop
  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 :
Methods code
sub _type_stamp {
    return '__EMBL_FLAT__'; # What kind of index are we?
sub _version {
    return 0.1;
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 my $EMBL, '<', $file or $self->throw("Can't open file for read : $file"); # Main indexing loop
$id = undef; @accs = (); while (<$EMBL>) { if( m{^//} ) { 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 $EMBL; return 1;
sub _file_format {
   my ($self,@args) = @_;

   return 'EMBL';

General documentation
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AUTHOR - Ewan BirneyTop
Email -
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _