Bio::Assembly::SingletUser Contributed Perl DocumentaBio::Assembly::Singlet(3)NAMEBio::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( -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:
http://bugzilla.open-bio.org/
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 object
_seq_to_singlet
Title : _seq_to_singlet
Usage : $singlet->seqref($seq)
Function: Transform a sequence into a singlet
Returns : A Bio::Assembly::Singlet object
Args : A Bio::Seq-compliant object
perl v5.14.1 2011-07-22 Bio::Assembly::Singlet(3)