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 sucess
Args : A Bio::Seq-compliant object