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Man Pages


Manual Reference Pages  -  BIO::ASSEMBLY::SINGLET (3)

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NAME

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

CONTENTS

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 sucess
    Args    : A Bio::Seq-compliant object



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perl v5.20.3 BIO::ASSEMBLY::SINGLET (3) 2016-04-05

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