# BioPerl module for FAST::Bio::Seq::LargeLocatableSeq
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Albert Vilella
#
# based on the FAST::Bio::LargePrimarySeq module
# by Ewan Birney <birney@sanger.ac.uk>
#
# and the FAST::Bio::LocatableSeq module
# by Ewan Birney <birney@sanger.ac.uk>
#
# Copyright Albert Vilella
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
FAST::Bio::Seq::LargeLocatableSeq - LocatableSeq object that stores sequence as
files in the tempdir
=head1 SYNOPSIS
# normal primary seq usage
use FAST::Bio::Seq::LargeLocatableSeq;
my $seq = FAST::Bio::Seq::LargeLocatableSeq->new(-seq => "CAGT-GGT",
-id => "seq1",
-start => 1,
-end => 7);
=head1 DESCRIPTION
FAST::Bio::Seq::LargeLocatableSeq - object with start/end points on it that
can be projected into a MSA or have coordinates relative to another
seq.
This object, unlike FAST::Bio::LocatableSeq, 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 crash your
machine. However, calls like $primary_seq-E<gt>subseq(10,100) will cause
only 90 characters to be brought into real memory.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
=head1 AUTHOR - Albert Vilella
Email avilella-AT-gmail-DOT-com
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
use vars qw($AUTOLOAD);
use strict;
use base qw(FAST::Bio::Seq::LargePrimarySeq FAST::Bio::LocatableSeq FAST::Bio::Root::IO);
=head2 new
Title : new
Usage : my $obj = FAST::Bio::Seq::LargeLocatableSeq->new();
Function: Builds a new FAST::Bio::Seq::LargeLocatableSeq object
Returns : an instance of FAST::Bio::Seq::LargeLocatableSeq
Args :
=cut
sub new {
my ($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);
my $mapping = exists $params{'-mapping'} ? $params{'-mapping'} : [1,1];
$self->mapping($mapping);
$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 $self;
}
=head2 length
Title : length
Usage :
Function:
Example :
Returns :
Args :
=cut
sub length {
my ($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 LargeLocatableSeq - 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('FAST::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('FAST::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 = FAST::Bio::PrimarySeq->new(-seq => $string)->revcom()->seq();
$string = FAST::Bio::Seq::LargePrimarySeq->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 = FAST::Bio::PrimarySeq->new(-seq => $string)->revcom()->seq();
$seq = FAST::Bio::Seq::LargePrimarySeq->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 : $seq->add_sequence_as_string("CATGAT");
Function: Appends additional residues to an existing LargeLocatableSeq object.
This allows one to build up a large sequence without storing
entire object in memory.
Returns : Current length of sequence
Args : string to append
=cut
sub add_sequence_as_string{
my ($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;