Raw content of Bio::Seq::LargePrimarySeq
<![CDATA[# $Id: LargePrimarySeq.pm,v 1.27 2002/12/01 00:05:21 jason Exp $
#
# BioPerl module for Bio::Seq::LargePrimarySeq
#
# Cared for by Ewan Birney <birney@ebi.ac.uk>
#
# Copyright Ewan Birney
#
# You may distribute this module under the same terms as perl itself
#
# updated to utilize File::Temp - jason 2000-12-12
# POD documentation - main docs before the code
=head1 NAME
Bio::Seq::LargePrimarySeq - PrimarySeq object that stores sequence as
files in the tempdir (as found by File::Temp) or the default method in
Bio::Root::Root
=head1 SYNOPSIS
# normal primary seq usage
=head1 DESCRIPTION
This object stores a sequence as a series of files in a temporary
directory. The aim is to allow someone the ability to store very large
sequences (eg, E<gt> 100MBases) in a file system without running out of memory
(eg, on a 64 MB real memory machine!).
Of course, to actually make use of this functionality, the programs
which use this object B<must> not call $primary_seq-E<gt>seq otherwise the
entire sequence will come out into memory and probably paste your
machine. However, calls $primary_seq-E<gt>subseq(10,100) will cause only
90 characters to be brought into real memory.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this
and other Bioperl modules. Send your comments and suggestions preferably
to one of the Bioperl mailing lists.
Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bio.perl.org/MailList.html - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via email
or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Ewan Birney, Jason Stajich
Email birney@ebi.ac.uk
Email jason@bioperl.org
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Seq::LargePrimarySeq;
use vars qw($AUTOLOAD @ISA);
use strict;
use Bio::PrimarySeq;
use Bio::Root::IO;
@ISA = qw(Bio::PrimarySeq Bio::Root::IO);
sub new {
my ($class, %params) = @_;
# don't let PrimarySeq set seq until we have
# opened filehandle
my $seq = $params{'-seq'} || $params{'-SEQ'};
if($seq ) {
delete $params{'-seq'};
delete $params{'-SEQ'};
}
my $self = $class->SUPER::new(%params);
$self->_initialize_io(%params);
my $tempdir = $self->tempdir( CLEANUP => 1);
my ($tfh,$file) = $self->tempfile( DIR => $tempdir );
$tfh && $self->_fh($tfh);
$file && $self->_filename($file);
$self->length(0);
$seq && $self->seq($seq);
return $self;
}
sub length {
my ($obj,$value) = @_;
if( defined $value) {
$obj->{'length'} = $value;
}
return (defined $obj->{'length'}) ? $obj->{'length'} : 0;
}
=head2 seq
Title : seq
Usage :
Function:
Example :
Returns :
Args :
=cut
sub seq {
my ($self, $data) = @_;
if( defined $data ) {
if( $self->length() == 0) {
$self->add_sequence_as_string($data);
} else {
$self->warn("Trying to reset the seq string, cannot do this with a LargePrimarySeq - must allocate a new object");
}
}
return $self->subseq(1,$self->length);
}
=head2 subseq
Title : subseq
Usage :
Function:
Example :
Returns :
Args :
=cut
sub subseq{
my ($self,$start,$end) = @_;
my $string;
my $fh = $self->_fh();
if( ref($start) && $start->isa('Bio::LocationI') ) {
my $loc = $start;
if( $loc->length == 0 ) {
$self->warn("Expect location lengths to be > 0");
return '';
} elsif( $loc->end < $loc->start ) {
# what about circular seqs
$self->warn("Expect location start to come before location end");
}
my $seq = '';
if( $loc->isa('Bio::Location::SplitLocationI') ) {
foreach my $subloc ( $loc->sub_Location ) {
if(! seek($fh,$subloc->start() - 1,0)) {
$self->throw("Unable to seek on file $start:$end $!");
}
my $ret = read($fh, $string, $subloc->length());
if( !defined $ret ) {
$self->throw("Unable to read $start:$end $!");
}
if( $subloc->strand < 0 ) {
$string = Bio::PrimarySeq->new(-seq => $string)->revcom()->seq();
}
$seq .= $string;
}
} else {
if(! seek($fh,$loc->start()-1,0)) {
$self->throw("Unable to seek on file ".$loc->start.":".
$loc->end ." $!");
}
my $ret = read($fh, $string, $loc->length());
if( !defined $ret ) {
$self->throw("Unable to read ".$loc->start.":".
$loc->end ." $!");
}
$seq = $string;
}
if( defined $loc->strand &&
$loc->strand < 0 ) {
$seq = Bio::PrimarySeq->new(-seq => $seq)->revcom()->seq();
}
return $seq;
}
if( $start <= 0 || $end > $self->length ) {
$self->throw("Attempting to get a subseq out of range $start:$end vs ".
$self->length);
}
if( $end < $start ) {
$self->throw("Attempting to subseq with end ($end) less than start ($start). To revcom use the revcom function with trunc");
}
if(! seek($fh,$start-1,0)) {
$self->throw("Unable to seek on file $start:$end $!");
}
my $ret = read($fh, $string, $end-$start+1);
if( !defined $ret ) {
$self->throw("Unable to read $start:$end $!");
}
return $string;
}
=head2 add_sequence_as_string
Title : add_sequence_as_string
Usage : $seq->add_sequence_as_string("CATGAT");
Function: Appends additional residues to an existing LargePrimarySeq object.
This allows one to build up a large sequence without storing
entire object in memory.
Returns : Current length of sequence
Args : string to append
=cut
sub add_sequence_as_string{
my ($self,$str) = @_;
my $len = $self->length + CORE::length($str);
my $fh = $self->_fh();
if(! seek($fh,0,2)) {
$self->throw("Unable to seek end of file: $!");
}
$self->_print($str);
$self->length($len);
}
=head2 _filename
Title : _filename
Usage : $obj->_filename($newval)
Function:
Example :
Returns : value of _filename
Args : newvalue (optional)
=cut
sub _filename{
my ($obj,$value) = @_;
if( defined $value) {
$obj->{'_filename'} = $value;
}
return $obj->{'_filename'};
}
=head2 alphabet
Title : alphabet
Usage : $obj->alphabet($newval)
Function:
Example :
Returns : value of alphabet
Args : newvalue (optional)
=cut
sub alphabet{
my ($self,$value) = @_;
if( defined $value) {
$self->SUPER::alphabet($value);
}
return $self->SUPER::alphabet() || 'dna';
}
sub DESTROY {
my $self = shift;
my $fh = $self->_fh();
close($fh) if( defined $fh );
# this should be handled by Tempfile removal, but we'll unlink anyways.
unlink $self->_filename() if defined $self->_filename() && -e $self->_filename;
$self->SUPER::DESTROY();
}
1;
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