Bio::Tools::Run::PiseApplication::merger.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::merger

SYNOPSIS

   #

DESCRIPTION

Bio::Tools::Run::PiseApplication::merger 
       Bioperl class for:
 
         MERGER  Merge two overlapping nucleic acid sequences (EMBOSS)
 
 
       Parameters: 
 
         (see also:
           http://bioweb.pasteur.fr/seqanal/interfaces/merger.html 
          for available values):
 
 
                 merger (String)
 
                 init (String)
 
                 seqa (Sequence)
                         seqa -- DNA [single sequence] (-seqa)
                         pipe: seqfile
 
                 seqb (Sequence)
                         seqb -- DNA [single sequence] (-seqb)
 
                 datafile (Excl)
                         Matrix file (-datafile)
 
                 gapopen (Float)
                         Gap opening penalty (-gapopen)
 
                 gapextend (Float)
                         Gap extension penalty (-gapextend)
 
                 outseq (OutFile)
                         outseq (-outseq)
                         pipe: seqfile
 
                 outseq_sformat (Excl)
                         Output format for: outseq
 
                 outfile (OutFile)
                         Output alignment and explanation (-outfile)
                         pipe: readseq_ok_alig
 
                 outfile_aformat (Excl)
                         Alignment output format (-aformat)
 
                 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/merger.html
•
Bio::Tools::Run::PiseApplication
•
Bio::Tools::Run::AnalysisFactory::Pise
•
Bio::Tools::Run::PiseJob

new

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