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

Langue: en

Autres versions - même langue

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

Section: 3 (Bibliothèques de fonctions)

Sommaire

NAME

Bio::Tools::Run::PiseApplication::coderet

SYNOPSIS

   #

DESCRIPTION

Bio::Tools::Run::PiseApplication::coderet 
       Bioperl class for:
 
         CODERET Extract CDS, mRNA and translations from feature tables (EMBOSS)
 
 
       Parameters: 
 
         (see also:
           http://bioweb.pasteur.fr/seqanal/interfaces/coderet.html 
          for available values):
 
 
                 coderet (String)
 
                 init (String)
 
                 seqall (Sequence)
                         seqall -- DNA [sequences] (-seqall)
                         pipe: seqsfile
 
                 cds (Switch)
                         Extract CDS sequences (-cds)
 
                 mrna (Switch)
                         Extract mrna sequences (-mrna)
 
                 translation (Switch)
                         Extract translated sequences (-translation)
 
                 seqout (OutFile)
                         seqout (-seqout)
                         pipe: seqfile
 
                 seqout_sformat (Excl)
                         Output format for: seqout
 
                 auto (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/coderet.html
•
Bio::Tools::Run::PiseApplication
•
Bio::Tools::Run::AnalysisFactory::Pise
•
Bio::Tools::Run::PiseJob

new

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