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Bio::Assembly::Singlet.3pm
Langue: en
Version: 2010-05-19 (ubuntu - 24/10/10)
Section: 3 (Bibliothèques de fonctions)
Sommaire
NAME
Bio::Assembly::Singlet - Perl module to hold and manipulatesinglets 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.comAPPENDIX
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
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