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Summary

Bio::Assembly::Singlet - Perl module to hold and manipulate
singlets from sequence assembly contigs.

Package variables

Included modules

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

Methods description

    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

    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

    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

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;

}

sub seqref {

    my ($self,$seq) = @_;
    if (defined $seq) { $self->_seq_to_singlet($seq) };
    return $self->{'_seqref'};

}

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

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

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.

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/

bioinformatics1 at dieselwurks.com

The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _