Bio::Index GenBank
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Bio::Index::GenBank - Interface for indexing one or more GenBank
files (i.e. flat file GenBank format).
Package variables
No package variables defined.
Included modules
    # Complete code for making an index for one or more GenBank files
use strict;
use Bio::Index::GenBank;
my $Index_File_Name = shift; my $inx = Bio::Index::GenBank->new(-filename => $Index_File_Name, -write_flag => 'WRITE'); $inx->make_index(@ARGV); # Print out sequences present in the index in gcg format use Bio::Index::GenBank; use Bio::SeqIO; use strict; my $Index_File_Name = shift; my $inx = Bio::Index::GenBank->new(-filename => $Index_File_Name); my $seqio = Bio::SeqIO->new(-format => 'gcg'); foreach my $id (@ARGV) { my $seq = $inx->fetch($id); # Returns Bio::Seq object $seqio->write_seq($seq); } # alternatively my ($locus, $acc); my $seq1 = $inx->get_Seq_by_id($locus); my $seq2 = $inx->get_Seq_by_acc($acc);
By default the index that is created uses the LOCUS, ACCESSION, and
VERSION identifiers as keys. Inherits functions for managing dbm
files from, and provides the basic
functionality for indexing GenBank files, and retrieving the
sequence from them. For best results 'use strict'.
You can also set or customize the unique key used to retrieve by
writing your own function and calling the id_parser() method.
For example:
# make the index
# here is where the retrieval key is specified sub get_id { my $line = shift; $line =~ /clone="(\S+)"/; $1; }
No description
No description
Methods description
_index_filecode    nextTop
  Title   : _index_file
Usage : $index->_index_file($file_name, $i)
Function: Specialized function to index GenBank format files.
Is provided with a filename and an integer
by make_index in its SUPER class.
Example :
Returns :
Args :
  Title   : id_parser
Usage : $index->id_parser( CODE )
Function: Stores or returns the code used by record_id to
parse the ID for record from a string.
Returns \&default_id_parser (see below) if not
set. An entry will be added to
the index for each string in the list returned.
Example : $index->id_parser( \&my_id_parser )
Returns : reference to CODE if called without arguments
Args : CODE
  Title   : default_id_parser
Usage : $id = default_id_parser($line)
Function: The default parser for
Returns : Array of specified ids
Args : a line string
 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 '__GenBank_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 = 0; my $id_parser = $self->id_parser; open my $GENBANK, '<', $file or $self->throw("Can't open file for read : $file"); my %done_ids; while (<$GENBANK>) { if (/^LOCUS/) { $begin = tell($GENBANK) - length($_); } for my $id (&$id_parser($_)) { next if exists $done_ids{$id}; $self->add_record($id, $i, $begin) if $id; $done_ids{$id} = 1; } if (m{//}) { %done_ids = (); } } close $GENBANK; return 1;
sub id_parser {
    my ($self,$code) = @_;

    if ($code) {
	$self->{'_id_parser'} = $code;
    return $self->{'_id_parser'} ||\& default_id_parser;
sub default_id_parser {
    my $line = shift;
    my %accs;
    if ( $line =~ /^LOCUS\s+(\S+)/ ) {
    } elsif ( $line =~ /^ACCESSION\s+(.*)/ ) {
	for my $acc ( split(/\s+/,$1) ) {
    } elsif ( /^VERSION\s+(.*)/) {	
	my $x = $1;
	for my $acc ( split(/\s+/,$1) ) {
	    $acc=~ s/GI\://;
    keys %accs;
sub _file_format {
   my ($self,@args) = @_;
   return 'GenBank';


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
Support Top
Please direct usage questions or support issues to the mailing list:
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
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
the web:
AUTHOR - Ewan BirneyTop
Email -
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _