NAME

Bio::Tools::Run::PiseApplication::abiview

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::abiview

      Bioperl class for:

        ABIVIEW Reads ABI file and display the trace (EMBOSS)


      Parameters: 

        (see also:
          http://bioweb.pasteur.fr/seqanal/interfaces/abiview.html 
         for available values):


                abiview (String)

                init (String)

                fname (InFile)
                        Name of the ABI trace file (-fname)

                outseq (OutFile)
                        Sequence file (-outseq)
                        pipe: seqfile

                outseq_sformat (Excl)
                        Output format for: Sequence file

                graph (Excl)
                        graph (-graph)

                startbase (Integer)
                        First base to report or display (-startbase)

                endbase (Integer)
                        Last base to report or display (-endbase)

                separate (Switch)
                        Separate the trace graphs for the 4 bases (-separate)

                yticks (Switch)
                        Display y-axis ticks (-yticks)

                sequence (Switch)
                        Display the sequence on the graph (-sequence)

                window (Integer)
                        Sequence display window size (-window)

                bases (String)
                        Base graphs to be displayed (-bases)

                auto (String)

                psouput (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

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/abiview.html
• Bio::Tools::Run::PiseApplication
• Bio::Tools::Run::AnalysisFactory::Pise
• Bio::Tools::Run::PiseJob

new

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