Christopher Fields > BioPerl-1.6.922 > Bio::Assembly::Singlet

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Module Version: 1.006922   Source   Latest Release: BioPerl-1.6.924

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://redmine.open-bio.org/projects/bioperl/

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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