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 = new Bio::Assembly::IO(-file=>"test.ace.1",
                               -format=>'phrap');

    $assembly = $aio->next_assembly;
    foreach $singlet ($assembly->all_singlets) {
      # do something
    }

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

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 _

seq_to_singlet

    Title   : seq_to_singlet
    Usage   : my $singlet = $io->seq_to_singlet($seq)
    Function: Wrap the information for a singlet as a Bio::Assembly::Singlet
    Returns : A Bio::Assembly::Singlet object
    Args    : A Bio::Seq-compliant object

id

    Title   : id
    Usage   : my $id = $singlet->id('chad matsalla')
    Function: 
    Returns : 
    Args    : 

seqref

    Title   : seqref
    Usage   : my $seqref = $singlet->seqref($seq);
    Function: Set the sequence to which this Singlet refers
    Returns : A Bio::Seq-compliant object
    Args    : 

chromatfilename

    Title   : chromatfilename
    Usage   : my $chromatfilename = $singlet->chromatfilename($newfilename);
    Function: Get the name of the chromatfile for this singlet
    Returns : A string.
    Args    : If a string is provided, the chromatfilename will be set to that value.

phdfilename

    Title   : phdfilename
    Usage   : my $phdfilename = $singlet->phdfilename($newfilename);
    Function: Get the name of the phdfile for this singlet
    Returns : A string.
    Args    : If a string is provided, the phdfilename will be set to that value.