Bio::Seq
LargePrimarySeq
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Summary
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
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
# normal primary seq usage
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, > 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 must not call $primary_seq->seq otherwise the
entire sequence will come out into memory and probably paste your
machine. However, calls $primary_seq->subseq(10,100) will cause only
90 characters to be brought into real memory.
Methods
Methods description
Title : _filename
Usage : $obj->_filename($newval)
Function:
Example :
Returns : value of _filename
Args : newvalue (optional) |
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 |
Title : alphabet
Usage : $obj->alphabet($newval)
Function:
Example :
Returns : value of alphabet
Args : newvalue (optional) |
Title : seq
Usage :
Function:
Example :
Returns :
Args : |
Title : subseq
Usage :
Function:
Example :
Returns :
Args : |
Methods code
sub DESTROY
{ my $self = shift;
my $fh = $self->_fh();
close($fh) if( defined $fh );
unlink $self->_filename() if defined $self->_filename() && -e $self->_filename;
$self->SUPER::DESTROY();
}
1;} | sub _filename
{ my ($obj,$value) = @_;
if( defined $value) {
$obj->{'_filename'} = $value;
}
return $obj->{'_filename'};} | sub add_sequence_as_string
{ my ($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);} | sub alphabet
{ my ($self,$value) = @_;
if( defined $value) {
$self->SUPER::alphabet($value);
}
return $self->SUPER::alphabet() || 'dna';} | sub length
{ my ($obj,$value) = @_;
if( defined $value) {
$obj->{'length'} = $value;
}
return (defined $obj->{'length'}) ? $obj->{'length'} : 0;} | sub new
{ my ($class, %params) = @_;
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 $self;} | sub seq
{ my ($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);} | 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 ) {
$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;} | General documentation
User feedback is an integral part of the evolution of this
and other Bioperl modules. Send your comments and suggestions preferably
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Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
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| AUTHOR - Ewan Birney, Jason Stajich | Top |
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _