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.
Inherit
Bio::PrimarySeq Bio::Root::IO Bio::Seq::LargeSeqI
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
new
No description
Code
lengthDescriptionCode
seqDescriptionCode
subseqDescriptionCode
add_sequence_as_stringDescriptionCode
_filenameDescriptionCode
alphabetDescriptionCode
DESTROY
No description
Code
Methods description
lengthcode    nextTop
 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 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
_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); $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 $self;
}
lengthdescriptionprevnextTop
sub length {
   my ($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 LargePrimarySeq - 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(); } $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 $string;
}
add_sequence_as_stringdescriptionprevnextTop
sub add_sequence_as_string {
   my ($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; # remove tempdirs as well
rmdir $self->{tempdir} if defined $self->{tempdir} && -e $self->{tempdir}; $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 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
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
the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Ewan Birney, Jason StajichTop
Email birney@ebi.ac.uk
Email jason@bioperl.org
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _