Bio::Seq LargeSeq
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Summary
Bio::Seq::LargeSeq - SeqI compliant object that stores sequence as
files in /tmp
Package variables
No package variables defined.
Included modules
Bio::Seq::LargePrimarySeq
Inherit
Bio::Seq 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
truncDescriptionCode
add_sequence_as_stringDescriptionCode
Methods description
trunccode    nextTop
 Title   : trunc
Usage : $subseq = $myseq->trunc(10,100);
Function: Provides a truncation of a sequence,
Example : Returns : a fresh Bio::SeqI object Args :
add_sequence_as_stringcodeprevnextTop
 Title   : add_sequence_as_string
Usage : $seq->add_sequence_as_string("CATGAT");
Function: Appends additional residues to an existing LargePrimarySeq object.
This allows one to build up a large sequence without storing
entire object in memory.
Returns : Current length of sequence
Args : string to append
Methods code
newdescriptionprevnextTop
sub new {
    my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);

    my ($pseq) = $self->_rearrange([qw(PRIMARYSEQ)], @args);

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

    return $self;
}
truncdescriptionprevnextTop
sub trunc {
    my ($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,$e));
}
add_sequence_as_stringdescriptionprevnextTop
sub add_sequence_as_string {
    my ($self,$str) = @_;
    return $self->primary_seq->add_sequence_as_string($str);
}

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 BirneyTop
Email birney@ebi.ac.uk
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
Bio::Seq::LargePrimarySeq methodsTop