Bio::Tools::Run::PiseApplication::grailclnt.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::grailclnt

SYNOPSIS

   #
 
 

DESCRIPTION

Bio::Tools::Run::PiseApplication::grailclnt
       Bioperl class for:
 
         GRAILCLNT       Grail client (Xu, Einstein, Mural, Shah, Uberbacher)
 
         References:
 
                 Xu, Y., Einstein, J. R., Mural, R.J., Shah, M. and Uberbacher, E.C., (1994) An Improved System for Exon Recognition and Gene Modeling in Human DNA Sequences, Published Presentation: The Second International Conference on Intelligent Systems for Molecular Biology, Stanford University, San Francisco, CA, August 14-17, 1994.
 
 
 
       Parameters: 
 
         (see also:
           http://bioweb.pasteur.fr/seqanal/interfaces/grailclnt.html 
          for available values):
 
 
                 grailclnt (String)
 
                 seq (Sequence)
                         Sequence
 
                 feature (Excl)
                         Which feature?
 
                 organism (Excl)
                         Organism
 
                 header (Switch)
                         Header
 
                 translation (Switch)
                         Translation
 
                 strandscores (Switch)
                         Strandscores (grail1)
 
                 shadowexons (Switch)
                         Shadowexons (grail 1.a or grail2)
 
                 clusters (Switch)
                         Clusters (grail 2)
 
                 cluster_file (InFile)
                         grail2exons results file
                         pipe: grail_cluster
 
                 modelexon_translation (Switch)
                         Gene model exons translation
 
                 genemodel_translation (Switch)
                         Entire gene models translation
 
                 auto_strand (Switch)
                         AUTO STRAND
 
                 start_strand (Integer)
                         AUTO STRAND start
 
                 end_strand (Integer)
                         AUTO STRAND end
 
                 forward_strand (Switch)
                         FORWARD_STRAND
 
                 reverse_strand (Switch)
                         REVERSE_STRAND
 
                 grail2_file (InFile)
                         grail2exons results file
                         pipe: grail_cluster
 
                 fserr_strand (Excl)
                         Strand
 
                 rpttv_organism (String)
 
                 start_seq (String)
 
                 end_seq (String)
 
                 end_request (String)
 
                 outfile (OutFile)
                         Result file
                         pipe: grail_cluster
 
 

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

new

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