Bio::Assembly::Singlet(3)

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

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.

FEEDBACK

  Mailing Lists
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
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 Bugs
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://github.com/bioperl/bioperl-live/issues

AUTHOR - Chad S. Matsalla
bioinformatics1 at dieselwurks.com

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

  new
    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

  seqref
    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_singlet
    Title   : _seq_to_singlet
    Usage   : $singlet->seqref($seq)
    Function: Transform a sequence into a singlet
    Returns : 1 for success
    Args    : A Bio::Seq-compliant object