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::Assembly::Contig Bio::Root::Root

Synopsis

    # Module loading
    use Bio::Assembly::IO;

    # Assembly loading methods
    $aio = new Bio::Assembly::IO(-file=>"test.ace.1",
                               -format=>'phrap');

    $assembly = $aio->next_assembly;
    foreach $singlet ($assembly->all_singlets) {
      # do something
    }

Description

A singlet is a sequence that phrap was unable to align to any other sequences.

Methods

Methods description

    Title   : seq_to_singlet
    Usage   : my $singlet = $io->seq_to_singlet($seq)
    Function: Wrap the information for a singlet as a Bio::Assembly::Singlet
    Returns : A Bio::Assembly::Singlet object
    Args    : A Bio::Seq-compliant object

    Title   : id
    Usage   : my $id = $singlet->id('chad matsalla')
    Function: 
    Returns : 
    Args    :

    Title   : seqref
    Usage   : my $seqref = $singlet->seqref($seq);
    Function: Set the sequence to which this Singlet refers
    Returns : A Bio::Seq-compliant object
    Args    :

    Title   : chromatfilename
    Usage   : my $chromatfilename = $singlet->chromatfilename($newfilename);
    Function: Get the name of the chromatfile for this singlet
    Returns : A string.
    Args    : If a string is provided, the chromatfilename will be set to that value.

    Title   : phdfilename
    Usage   : my $phdfilename = $singlet->phdfilename($newfilename);
    Function: Get the name of the phdfile for this singlet
    Returns : A string.
    Args    : If a string is provided, the phdfilename will be set to that value.

Methods code

sub new {

     my ($class,%ARG) = @_;
     my $self = $class->SUPER::new(%ARG);
     my $args =\% ARG;
     bless ($self,$class);
     if ($args->{'-seq'}) {
          $self->seq_to_singlet($args->{'-seq'});
     }
     return $self;

}

sub seq_to_singlet {

    my ($self,$seq) = @_;
    $self->seqref($seq);
    $self->strand(1);
     my $lseq = new Bio::LocatableSeq(
               -seq =>   $seq->seq(),
               -start    =>   1,
               -end =>   $seq->length(),
               -id  =>   $seq->display_id());
     $lseq->{chromatfilename} = $seq->{'chromatfilename'};
     $lseq->{phdfilename} = $seq->{'phdfilename'};
     $self->set_consensus_sequence($lseq);
     if (UNIVERSAL::isa($seq,"Bio::Seq::Quality")) {
          $self->set_consensus_quality($seq)
     }
     else {
          # print("seq_to_singlet: the sequence (".$seq->desc().") is not a Bio::Seq::quality. it is this ($seq)\n");
     }
     $self->add_seq($lseq);

}

sub id {

     my $self = shift;
     # print("Getting the id for this thing:\n");
     # $dumper->dumpValue($self->seqref());
     # print("This is the id: (".$self->seqref()->id().")\n");
     return $self->seqref()->id();

}

sub seqref {

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

}

sub chromatfilename {

     my ($self,$name) = @_;
     if ($name) { $self->{'chromatfilename'} = $name; }
     return $self->{'chromatfilename'};

}

sub phdfilename {

     my ($self,$name) = @_;
     if ($name) { $self->{phdfilename} = $name; }
     return $self->{'phdfilename'};

}

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

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:

  http://bugzilla.open-bio.org/

bioinformatics1 at dieselwurks.com

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