Bio::Seq LargeLocatableSeq
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Summary
Bio::Seq::LargeLocatableSeq - LocatableSeq object that stores sequence as
files in the tempdir
Package variables
No package variables defined.
Inherit
Bio::LocatableSeq Bio::Root::IO Bio::Seq::LargePrimarySeq
Synopsis
  # normal primary seq usage
use Bio::Seq::LargeLocatableSeq;
my $seq = Bio::Seq::LargeLocatableSeq->new(-seq => "CAGT-GGT",
-id => "seq1",
-start => 1,
-end => 7);
Description
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 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, > 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 crash your
machine. However, calls like $primary_seq->subseq(10,100) will cause
only 90 characters to be brought into real memory.
Methods
newDescriptionCode
lengthDescriptionCode
seqDescriptionCode
subseqDescriptionCode
add_sequence_as_stringDescriptionCode
_filenameDescriptionCode
alphabetDescriptionCode
DESTROY
No description
Code
Methods description
newcode    nextTop
 Title   : new
Usage : my $obj = Bio::Seq::LargeLocatableSeq->new();
Function: Builds a new Bio::Seq::LargeLocatableSeq object
Returns : an instance of Bio::Seq::LargeLocatableSeq
Args :
lengthcodeprevnextTop
 Title   : length
Usage :
Function:
Example :
Returns :
Args :
seqcodeprevnextTop
 Title   : seq
Usage :
Function:
Example :
Returns :
Args :
subseqcodeprevnextTop
 Title   : subseq
Usage :
Function:
Example :
Returns :
Args :
add_sequence_as_stringcodeprevnextTop
 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
_filenamecodeprevnextTop
 Title   : _filename
Usage : $obj->_filename($newval)
Function:
Example :
Returns : value of _filename
Args : newvalue (optional)
alphabetcodeprevnextTop
 Title   : alphabet
Usage : $obj->alphabet($newval)
Function:
Example :
Returns : value of alphabet
Args : newvalue (optional)
Methods code
newdescriptionprevnextTop
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 $self;
}
lengthdescriptionprevnextTop
sub length {
   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'length'} = $value;
    }

    return (defined $obj->{'length'}) ? $obj->{'length'} : 0;
}
seqdescriptionprevnextTop
sub seq {
   my ($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);
}
subseqdescriptionprevnextTop
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();
$string = 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 = Bio::PrimarySeq->new(-seq => $string)->revcom()->seq();
$seq = 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 $string;
}
add_sequence_as_stringdescriptionprevnextTop
sub add_sequence_as_string {
   my ($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);
}
_filenamedescriptionprevnextTop
sub _filename {
   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'_filename'} = $value;
    }
    return $obj->{'_filename'};
}
alphabetdescriptionprevnextTop
sub alphabet {
   my ($self,$value) = @_;
   if( defined $value) {
      $self->SUPER::alphabet($value);
    }
    return $self->SUPER::alphabet() || 'dna';
}
DESTROYdescriptionprevnextTop
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;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
Support Top
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.
Reporting BugsTop
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:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Albert VilellaTop
Email avilella-AT-gmail-DOT-com
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _