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Summary

Bio::Seq::LargeSeq - SeqI compliant object that stores sequence as files in /tmp

Package variables

Included modules

Inherit

Bio::Seq

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   : 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   : trunc
 Usage   : $subseq = $myseq->trunc(10,100);
 Function: Provides a truncation of a sequence,

 Example :
 Returns : a fresh Bio::SeqI object
 Args    :

Methods code

sub add_sequence_as_string {

    my ($self,$str) = @_;
    return $self->primary_seq->add_sequence_as_string($str);
}

1;

}

sub new {

    my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);
    
    my ($pseq) = $self->_rearrange([qw(PRIMARYSEQ)], @args);

    if( ! defined $pseq ) {
	$pseq = new Bio::Seq::LargePrimarySeq(@args);
    }
    $self->primary_seq($pseq);

    return $self;

}

sub trunc {

    my ($self, $s, $e) = @_;
    return new Bio::Seq::LargeSeq(
				  '-display_id' => $self->display_id,
				  '-accession_number' => $self->accession_number,
				  '-desc' => $self->desc,
				  '-alphabet' => $self->alphabet,
				  -primaryseq => 
				  $self->primary_seq->trunc($s,$e));

}

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://www.bioperl.org/MailList.html             - About the mailing lists

Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.
Bug reports can be submitted via email or the web:

  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/

Email birney@ebi.ac.uk

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _