Raw content of Bio::Seq::LargeSeq # $Id: LargeSeq.pm,v 1.11 2002/10/22 07:38:40 lapp Exp $ # # BioPerl module for Bio::Seq::LargeSeq # # Cared for by Ewan Birney, Jason Stajich # # Copyright Ewan Birney, Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Seq::LargeSeq - SeqI compliant object that stores sequence as files in /tmp =head1 SYNOPSIS # normal primary seq usage =head1 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, E<gt> 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 B<must> not call $primary_seq-E<gt>seq otherwise the entire sequence will come out into memory and probably paste your machine. However, calls $primary_seq-E<gt>subseq(10,100) will cause only 90 characters to be brought into real memory. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://www.bioperl.org/MailList.html - About the mailing lists =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ =head1 AUTHOR - Ewan Birney Email birney@ebi.ac.uk =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Seq::LargeSeq; use vars qw($AUTOLOAD @ISA); use strict; # Object preamble - inherits from Bio::Root::Objecttest 8, use Bio::Seq::LargePrimarySeq; use Bio::Seq; @ISA = qw(Bio::Seq); 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; } =head2 trunc Title : trunc Usage : $subseq = $myseq->trunc(10,100); Function: Provides a truncation of a sequence, Example : Returns : a fresh Bio::SeqI object Args : =cut sub trunc { my ($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)); } =head2 Bio::Seq::LargePrimarySeq methods =cut =head2 add_sequence_as_string Title : add_sequence_as_string Usage : $seq->add_sequence_as_string("CATGAT"); Function: Appends additional residues to an existing LargePrimarySeq object. This allows one to build up a large sequence without storing entire object in memory. Returns : Current length of sequence Args : string to append =cut sub add_sequence_as_string { my ($self,$str) = @_; return $self->primary_seq->add_sequence_as_string($str); } 1;