Bio::Tools::Run::PiseApplication::cpgplot.3pm

Langue: en

Autres versions - même langue

Version: 2008-11-10 (debian - 07/07/09)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Tools::Run::PiseApplication::cpgplot

SYNOPSIS

   #
 
 

DESCRIPTION

Bio::Tools::Run::PiseApplication::cpgplot
       Bioperl class for:
 
         CPGPLOT Plot CpG rich areas (EMBOSS)
 
 
       Parameters: 
 
         (see also:
           http://bioweb.pasteur.fr/seqanal/interfaces/cpgplot.html 
          for available values):
 
 
                 cpgplot (String)
 
                 init (String)
 
                 sequence (Sequence)
                         sequence -- DNA [sequences] (-sequence)
                         pipe: seqsfile
 
                 window (Integer)
                         Window size (-window)
 
                 shift (Integer)
                         Window shift increment (-shift)
 
                 minlen (Integer)
                         Minimum length of an island (-minlen)
 
                 minoe (Float)
                         Minimum observed/expected (-minoe)
 
                 minpc (Float)
                         Minimum percentage (-minpc)
 
                 outfile (OutFile)
                         outfile (-outfile)
 
                 graph (Excl)
                         graph (-graph)
 
                 obsexp (Switch)
                         Show observed/expected threshold line (-obsexp)
 
                 cg (Switch)
                         Show CpG rich regions (-cg)
 
                 pc (Switch)
                         Show percentage line (-pc)
 
                 featout (OutFile)
                         feature file for output (-featout)
 
                 featout_offormat (Excl)
                         Feature output format (-offormat)
 
                 auto (String)
 
                 psouput (String)
 
 

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 list. 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 of the bugs and their resolution. Bug reports can be submitted via the web:
   http://bugzilla.open-bio.org/
 
 

AUTHOR

Catherine Letondal (letondal@pasteur.fr) Copyright (C) 2003 Institut Pasteur & Catherine Letondal. All Rights Reserved.

This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

DISCLAIMER

This software is provided ``as is'' without warranty of any kind.

SEE ALSO

http://bioweb.pasteur.fr/seqanal/interfaces/cpgplot.html
Bio::Tools::Run::PiseApplication
Bio::Tools::Run::AnalysisFactory::Pise
Bio::Tools::Run::PiseJob

new

  Title   : new()
  Usage   : my $cpgplot = Bio::Tools::Run::PiseApplication::cpgplot->new($location, $email, @params);
  Function: Creates a Bio::Tools::Run::PiseApplication::cpgplot object.
            This method should not be used directly, but rather by 
            a Bio::Tools::Run::AnalysisFactory::Pise instance.
            my $factory = Bio::Tools::Run::AnalysisFactory::Pise->new();
            my $cpgplot = $factory->program('cpgplot');
  Example : -
  Returns : An instance of Bio::Tools::Run::PiseApplication::cpgplot.