Bio::Tools::Run::PiseApplication::merger(3)

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/MailList.shtml  - 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 email or the web:

  bioperl-bugs@bioperl.org
  http://bioperl.org/bioperl-bugs/

AUTHOR
Catherine Letondal (letondal@pasteur.fr)

COPYRIGHT
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.