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