Bio::Assembly Singlet
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Summary
Bio::Assembly::Singlet - Perl module to hold and manipulate
singlets from sequence assembly contigs.
Package variables
No package variables defined.
Included modules
Bio::LocatableSeq
Bio::Seq::PrimaryQual
Bio::SeqFeature::Collection
Inherit
Bio::Align::AlignI Bio::Assembly::Contig Bio::Root::Root
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 );
Description
A singlet is a sequence that phrap was unable to align to any other sequences.
Methods
newDescriptionCode
seqrefDescriptionCode
_seq_to_singletDescriptionCode
Methods description
newcode    nextTop
    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
seqrefcodeprevnextTop
    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
_seq_to_singletcodeprevnextTop
    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
Methods code
newdescriptionprevnextTop
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 $self;
}
seqrefdescriptionprevnextTop
sub seqref {
    my ($self,$seq) = @_;
    if (defined $seq) { $self->_seq_to_singlet($seq) };
    return $self->{'_seqref'};
}
_seq_to_singletdescriptionprevnextTop
sub _seq_to_singlet {
    my ($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;
}
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 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 - Chad S. MatsallaTop
bioinformatics1 at dieselwurks.com
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _