Linux Certif

Toute la documentation sur la certification Linux LPI

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 = 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.