Bio::Seq
LargePrimarySeq
Toolbar
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.
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 : length
Usage :
Function:
Example :
Returns :
Args : |
Title : seq
Usage :
Function:
Example :
Returns :
Args : |
Title : subseq
Usage :
Function:
Example :
Returns :
Args : |
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 : _filename
Usage : $obj->_filename($newval)
Function:
Example :
Returns : value of _filename
Args : newvalue (optional) |
Title : alphabet
Usage : $obj->alphabet($newval)
Function:
Example :
Returns : value of alphabet
Args : newvalue (optional) |
Methods code
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 );
$self->{tempdir} = $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'}) ? $obj->{'length'} : 0;} | sub seq
{ my ($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 $string;} | sub add_sequence_as_string
{ my ($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 _filename
{ my ($obj,$value) = @_;
if( defined $value) {
$obj->{'_filename'} = $value;
}
return $obj->{'_filename'};} | sub alphabet
{ my ($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 );
unlink $self->_filename() if defined $self->_filename() && -e $self->_filename;
rmdir $self->{tempdir} if defined $self->{tempdir} && -e $self->{tempdir};
$self->SUPER::DESTROY();
}
1;} | General documentation
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
Please direct usage questions or support issues to the mailing list:
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.
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:
https://redmine.open-bio.org/projects/bioperl/
| AUTHOR - Ewan Birney, Jason Stajich | Top |
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _