Bio::Tools::Run::PiseApplication::checktrans.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::checktrans

SYNOPSIS

   #
 
 

DESCRIPTION

Bio::Tools::Run::PiseApplication::checktrans
       Bioperl class for:
 
         CHECKTRANS      Reports STOP codons and ORF statistics of a protein (EMBOSS)
 
 
       Parameters: 
 
         (see also:
           http://bioweb.pasteur.fr/seqanal/interfaces/checktrans.html 
          for available values):
 
 
                 checktrans (String)
 
                 init (String)
 
                 sequence (Sequence)
                         sequence -- stopprotein [sequences] (-sequence)
                         pipe: seqsfile
 
                 orfml (Integer)
                         Minimum ORF Length to report (-orfml)
 
                 report (OutFile)
                         report (-report)
 
                 outseq (OutFile)
                         Sequence file to hold output ORF sequences (-outseq)
                         pipe: seqsfile
 
                 outseq_sformat (Excl)
                         Output format for: Sequence file to hold output ORF sequences
 
                 featout (OutFile)
                         Feature file for output (-featout)
 
                 featout_offormat (Excl)
                         Feature output format (-offormat)
 
                 addlast (Switch)
                         Force the sequence to end with an asterisk (-addlast)
 
                 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/checktrans.html
Bio::Tools::Run::PiseApplication
Bio::Tools::Run::AnalysisFactory::Pise
Bio::Tools::Run::PiseJob

new

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