Christopher Fields > BioPerl-1.6.923 > Bio::Assembly::Singlet



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Source   Latest Release: BioPerl-1.6.924


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


    # 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.


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AUTHOR - Chad S. Matsalla ^

bioinformatics1 at


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


    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
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