Bio::Assembly::Singlet(3)                  User Contributed Perl Documentation




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-lATbioperl.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-lATbioperl.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 v5.12.2                                                 February 24, 2011