Provided by: libbio-perl-perl_1.7.2-3_all bug


       Bio::Assembly::Singlet - Perl module to hold and manipulate
                            singlets from sequence assembly contigs.


           # 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


       A singlet is a sequence that phrap was unable to align to any other sequences.


   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.
                  - General discussion  - About the mailing lists

       Please direct usage questions or support issues to the mailing list:

       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:

AUTHOR - Chad S. Matsalla

       bioinformatics1 at


       The rest of the documentation details each of the object methods. Internal methods are
       usually preceded with a _

           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

           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

           Title   : _seq_to_singlet
           Usage   : $singlet->seqref($seq)
           Function: Transform a sequence into a singlet
           Returns : 1 for success
           Args    : A Bio::Seq-compliant object