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
Bio::Seq::LargePrimarySeq
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
add_sequence_as_stringDescriptionCode
new
No description
Code
truncDescriptionCode
Methods description
add_sequence_as_stringcode    nextTop
 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
trunccodeprevnextTop
 Title   : trunc
Usage : $subseq = $myseq->trunc(10,100);
Function: Provides a truncation of a sequence,
Example : Returns : a fresh Bio::SeqI object Args :
Methods code
add_sequence_as_stringdescriptionprevnextTop
sub add_sequence_as_string {
    my ($self,$str) = @_;
    return $self->primary_seq->add_sequence_as_string($str);
}

1;
}
newdescriptionprevnextTop
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 $self;
}
truncdescriptionprevnextTop
sub trunc {
    my ($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));
}
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://www.bioperl.org/MailList.html - About the mailing lists
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 email or the web:
  bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
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