Raw content of Bio::Index::Fastq
<![CDATA[#
#
# BioPerl module for Bio::Index::Fastq
#
# Cared for by Tony Cox <avc@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::Fastq - Interface for indexing (multiple) fastq files
=head1 SYNOPSIS
# Complete code for making an index for several
# fastq files
use Bio::Index::Fastq;
use strict;
my $Index_File_Name = shift;
my $inx = Bio::Index::Fastq->new(
'-filename' => $Index_File_Name,
'-write_flag' => 1);
$inx->make_index(@ARGV);
# Print out several sequences present in the index
# in Fastq format
use Bio::Index::Fastq;
use strict;
my $Index_File_Name = shift;
my $inx = Bio::Index::Fastq->new('-filename' => $Index_File_Name);
my $out = Bio::SeqIO->new('-format' => 'Fastq','-fh' => \*STDOUT);
foreach my $id (@ARGV) {
my $seq = $inx->fetch($id); # Returns Bio::Seq::SeqWithQuality object
$out->write_seq($seq);
}
# or, alternatively
my $seq = $inx->get_Seq_by_id($id); #identical to fetch
=head1 DESCRIPTION
Inherits functions for managing dbm files from Bio::Index::Abstract.pm,
and provides the basic funtionallity for indexing fastq files, and
retrieving the sequence from them. Note: for best results 'use strict'.
Bio::Index::Fastq supports the Bio::DB::BioSeqI interface, meaning
it can be used as a Sequence database for other parts of bioperl
=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/MailList.shtml - 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
email or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Tony Cox
Email - avc@sanger.ac.uk
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Index::Fastq;
use vars qw($VERSION @ISA);
use strict;
use Bio::Index::AbstractSeq;
use Bio::Seq;
@ISA = qw(Bio::Index::AbstractSeq);
#
# Suggested fix by Michael G Schwern <schwern@pobox.com> to
# get around a clash with CPAN shell...
#
BEGIN {
$VERSION = 0.2;
}
sub _version {
return $VERSION;
}
=head2 _file_format
Title : _file_format
Function: The file format for this package, which is needed
by the SeqIO system when reading the sequence.
Returns : 'Fastq'
=cut
sub _file_format {
return 'Fastq';
}
=head2 _index_file
Title : _index_file
Usage : $index->_index_file( $file_name, $i )
Function: Specialist function to index FASTQ 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, # Offset from start of file of the start
# of the last found record.
);
$begin = 0;
my $id_parser = $self->id_parser;
my $c = 0;
open FASTQ, $file or $self->throw("Can't open file for read : $file");
# Main indexing loop
while (<FASTQ>) {
if (/^@/) {
# $begin is the position of the first character after the '@'
my $begin = tell(FASTQ) - length( $_ ) + 1;
foreach my $id (&$id_parser($_)) {
$self->add_record($id, $i, $begin);
$c++;
}
}
}
close FASTQ;
return ($c);
}
=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. Useful
for (for instance) specifying a different
parser for different flavours of FASTQ file.
Returns \&default_id_parser (see below) if not
set. If you supply your own id_parser
subroutine, then it should expect a fastq
description line. An entry will be added to
the index for each string in the list returned.
Example : $index->id_parser( \&my_id_parser )
Returns : ref 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( $header )
Function: The default Fastq ID parser for Fastq.pm
Returns $1 from applying the regexp /^>\s*(\S+)/
to $header.
Returns : ID string
Args : a fastq header line string
=cut
sub default_id_parser {
if ($_[0] =~ /^@\s*(\S+)/) {
return $1;
} else {
return;
}
}
1;
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