—————#
# $Id: GenBank.pm,v 1.23.4.1 2006/10/02 23:10:20 sendu Exp $
#
# BioPerl module for Bio::Index::Abstract
#
# Cared for by Ewan Birney <birney@sanger.ac.uk>
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Index::GenBank - Interface for indexing one or more GenBank
files (i.e. flat file GenBank format).
=head1 SYNOPSIS
# 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 = new Bio::SeqIO(-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);
=head1 DESCRIPTION
By default the index that is created uses the LOCUS, ACCESSION, and
VERSION identifiers as keys. Inherits functions for managing dbm
files from Bio::Index::Abstract.pm, 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:
$inx->id_parser(\&get_id);
# make the index
$inx->make_index($file_name);
# here is where the retrieval key is specified
sub get_id {
my $line = shift;
$line =~ /clone="(\S+)"/;
$1;
}
=head1 FEED_BACK
=head2 Mailing Lists
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.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Reporting Bugs
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:
=head1 AUTHOR - Ewan Birney
Email - birney@ebi.ac.uk
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let's begin the code...
package
Bio::Index::GenBank;
use
strict;
use
Bio::Seq;
sub
_type_stamp {
return
'__GenBank_FLAT__'
;
# What kind of index are we?
}
sub
_version {
return
0.1;
}
=head2 _index_file
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 :
=cut
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;
}
=head2 id_parser
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
=cut
sub
id_parser {
my
(
$self
,
$code
) =
@_
;
if
(
$code
) {
$self
->{
'_id_parser'
} =
$code
;
}
return
$self
->{
'_id_parser'
} || \
&default_id_parser
;
}
=head2 default_id_parser
Title : default_id_parser
Usage : $id = default_id_parser($line)
Function: The default parser for GenBank.pm
Returns : Array of specified ids
Args : a line string
=cut
#'
sub
default_id_parser {
my
$line
=
shift
;
my
%accs
;
if
(
$line
=~ /^LOCUS\s+(\S+)/ ) {
$accs
{$1}++;
}
elsif
(
$line
=~ /^ACCESSION\s+(.*)/ ) {
for
my
$acc
(
split
(/\s+/,$1) ) {
$accs
{
$acc
}++;
}
}
elsif
( /^VERSION\s+(.*)/) {
my
$x
= $1;
for
my
$acc
(
split
(/\s+/,$1) ) {
$acc
=~ s/GI\://;
$accs
{
$acc
}++;
}
}
keys
%accs
;
}
=head2 _file_format
Title : _file_format
Usage : Internal function for indexing system
Function: Provides file format for this database
Example :
Returns :
Args :
=cut
sub
_file_format{
my
(
$self
,
@args
) =
@_
;
return
'GenBank'
;
}
1;
__END__