NAME

Bio::Tools::Run::PiseApplication::compseq

SYNOPSIS

  #

DESCRIPTION

Bio::Tools::Run::PiseApplication::compseq

      Bioperl class for:

        COMPSEQ Counts the composition of dimer/trimer/etc words in a sequence (EMBOSS)


      Parameters: 

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


                compseq (String)

                init (String)

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

                word (Integer)
                        Word size to consider (e.g. 2=dimer) (-word)

                infile (InFile)
                        'compseq' file to use for expected word frequencies (-infile)

                frame (Integer)
                        Frame of word to look at (0=all frames) (-frame)

                ignorebz (Switch)
                        Ignore the amino acids B and Z and just count them as 'Other' (-ignorebz)

                reverse (Switch)
                        Count words in the forward and reverse sense (-reverse)

                outfile (OutFile)
                        outfile (-outfile)

                zerocount (Switch)
                        Display the words that have a frequency of zero (-zerocount)

                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

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/compseq.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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