NAME

Bio::Tools::Run::PiseApplication::notseq

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::notseq

      Bioperl class for:

        NOTSEQ  Excludes a set of sequences and writes out the remaining ones (EMBOSS)


      Parameters: 

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


                notseq (String)

                init (String)

                sequence (Sequence)
                        sequence [sequences] (-sequence)
                        pipe: seqsfile

                exclude (String)
                        Sequence names to exclude (-exclude)

                outseq (OutFile)
                        outseq (-outseq)
                        pipe: seqsfile

                outseq_sformat (Excl)
                        Output format for: outseq

                junkout (OutFile)
                        file of excluded sequences (-junkout)

                junkout_sformat (Excl)
                        Output format for: file of excluded sequences

                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/notseq.html

• Bio::Tools::Run::PiseApplication

• Bio::Tools::Run::AnalysisFactory::Pise

• Bio::Tools::Run::PiseJob

new

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