#
# BioPerl module for Bio::Assembly::Singlet
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Chad Matsalla <bioinformatics1 at dieselwurks.com>
#
# Copyright Chad Matsalla
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Assembly::Singlet - Perl module to hold and manipulate
singlets from sequence assembly contigs.
=head1 SYNOPSIS
# Module loading
use Bio::Assembly::IO;
# Assembly loading methods
$aio = Bio::Assembly::IO->new( -file => 'test.ace.1',
-format => 'phrap' );
$assembly = $aio->next_assembly;
foreach $singlet ($assembly->all_singlets) {
# do something
}
# OR, if you want to build the singlet yourself,
use Bio::Assembly::Singlet;
$singlet = Bio::Assembly::Singlet->new(
-id => 'Singlet1',
-seqref => $seq
);
=head1 DESCRIPTION
A singlet is a sequence that phrap was unable to align to any other sequences.
=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 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
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=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 the
web:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Chad S. Matsalla
bioinformatics1 at dieselwurks.com
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
#'
package Bio::Assembly::Singlet;
use strict;
use Bio::SeqFeature::Collection;
use Bio::LocatableSeq;
use Bio::Seq::PrimaryQual;
use base qw(Bio::Assembly::Contig Bio::Root::Root Bio::Align::AlignI);
=head2 new
Title : new
Usage : $singlet = $io->new( -seqref => $seq )
Function: Create a new singlet object
Returns : A Bio::Assembly::Singlet object
Args : -seqref => Bio::Seq-compliant sequence object for the singlet
=cut
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
my ($seqref) = $self->_rearrange([qw(SEQREF)], @args);
$self->{'_seqref'} = undef;
if (defined $seqref) {
$self->seqref($seqref);
}
return $self;
}
=head2 seqref
Title : seqref
Usage : $seqref = $singlet->seqref($seq);
Function: Get/set the sequence to which this singlet refers
Returns : A Bio::Seq-compliant object
Args : A Bio::Seq-compliant or Bio::Seq::Quality object
=cut
sub seqref {
my ($self,$seq) = @_;
if (defined $seq) { $self->_seq_to_singlet($seq) };
return $self->{'_seqref'};
}
=head2 _seq_to_singlet
Title : _seq_to_singlet
Usage : $singlet->seqref($seq)
Function: Transform a sequence into a singlet
Returns : 1 for sucess
Args : A Bio::Seq-compliant object
=cut
sub _seq_to_singlet {
my ($self, $seq) = @_;
# Object type checking
$self->throw("Unable to process non Bio::Seq-compliant object [".ref($seq)."]")
unless ( defined $seq && ($seq->isa('Bio::PrimarySeqI') || $seq->isa('Bio::Seq::Quality')) );
# Sanity check
$self->throw("Unable to have more than one sequence reference in a singlet")
if (defined $self->{'_seqref'});
# From sequence to locatable sequence
my $lseq = Bio::LocatableSeq->new(
-id => $seq->id,
-seq => $seq->seq,
-strand => $seq->isa('Bio::LocatableSeq') ? $seq->strand : 1,
-start => 1,
#-end => we let Bio::LocatableSeq calculate it (Seq and LocatableSeq)
);
# Add new sequence and its coordinates to the contig
my $lcoord = Bio::SeqFeature::Generic->new( -start => $lseq->start,
-end => $lseq->end );
$self->set_seq_coord( $lcoord, $lseq );
$self->{'_seqref'} = $lseq;
# Creating consensus
$self->set_consensus_sequence($lseq);
if ($seq->isa("Bio::Seq::Quality")) {
my $qual = Bio::Seq::PrimaryQual->new( -id => $seq->id,
-qual => $seq->qual );
$self->set_consensus_quality($qual);
}
return 1;
}
1;