Bio::Assembly Singlet
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Bio::Assembly::Singlet - Perl module to hold and manipulate
singlets from sequence assembly contigs.
Package variables
No package variables defined.
Included modules
Bio::Align::AlignI Bio::Assembly::Contig Bio::Root::Root
    # 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 );
A singlet is a sequence that phrap was unable to align to any other sequences.
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
    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) {
    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
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AUTHOR - Chad S. MatsallaTop
bioinformatics1 at
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