Bio::Tools::Run::PiseApplication::getorf.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::getorf

SYNOPSIS

   #
 
 

DESCRIPTION

Bio::Tools::Run::PiseApplication::getorf
       Bioperl class for:
 
         GETORF  Finds and extracts open reading frames (ORFs) (EMBOSS)
 
 
       Parameters: 
 
         (see also:
           http://bioweb.pasteur.fr/seqanal/interfaces/getorf.html 
          for available values):
 
 
                 getorf (String)
 
                 init (String)
 
                 sequence (Sequence)
                         sequence -- DNA [sequences] (-sequence)
                         pipe: seqsfile
 
                 table (Excl)
                         Code to use -- Genetic codes (-table)
 
                 minsize (Integer)
                         Minimum nucleotide size of ORF to report (-minsize)
 
                 find (Excl)
                         Type of output -- Type of sequence to output (-find)
 
                 methionine (Switch)
                         Change initial START codons to Methionine (-methionine)
 
                 circular (Switch)
                         Is the sequence circular (-circular)
 
                 reverse (Switch)
                         Find ORFs in the reverse sequence (-reverse)
 
                 flanking (Integer)
                         Number of flanking nucleotides to report (-flanking)
 
                 outseq (OutFile)
                         outseq (-outseq)
                         pipe: seqsfile
 
                 outseq_sformat (Excl)
                         Output format for: outseq
 
                 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/getorf.html
Bio::Tools::Run::PiseApplication
Bio::Tools::Run::AnalysisFactory::Pise
Bio::Tools::Run::PiseJob

new

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