Bio::Tools::Run::PiseApplication::cds.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::cds

SYNOPSIS

   #
 
 

DESCRIPTION

Bio::Tools::Run::PiseApplication::cds
       Bioperl class for:
 
         CDS     Search Coding Regions (F. Chauveau)
 
 
       Parameters: 
 
         (see also:
           http://bioweb.pasteur.fr/seqanal/interfaces/cds.html 
          for available values):
 
 
                 cds (String)
 
                 seq (Sequence)
                         Sequence File
 
                 minaa (Integer)
                         Minimum number of amino acids in CDS
 
                 frame (Excl)
                         Frame
 
                 starts (String)
                         START codons (separated by commas)
 
                 maxf (Switch)
                         longest CDS in each frame
 
                 max (Switch)
                         longest CDS
 
                 all (Switch)
                         all CDS, including CDS inside CDS
 
                 nucl (Switch)
                         nucleotids output
 
                 print_adn (Switch)
                         Print ADN as well as Amino-acids
 
                 left_adn (Integer)
                         How many base pairs on the left (if print ADN)
 
                 print_frame (Switch)
                         print frame before search
 
                 print_pos (Switch)
                         print only position(s)
 
                 xml (Switch)
                         XML output (-x)
 
                 xmldtdcopy (String)
 
                 end_stop (Switch)
                         CDS ends at STOP
 
                 genetic (Excl)
                         Genetic Code
 
 

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/cds.html
Bio::Tools::Run::PiseApplication
Bio::Tools::Run::AnalysisFactory::Pise
Bio::Tools::Run::PiseJob

new

  Title   : new()
  Usage   : my $cds = Bio::Tools::Run::PiseApplication::cds->new($location, $email, @params);
  Function: Creates a Bio::Tools::Run::PiseApplication::cds 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 $cds = $factory->program('cds');
  Example : -
  Returns : An instance of Bio::Tools::Run::PiseApplication::cds.