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Bio::Assembly::Singlet.3pm

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( -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