NAME

Bio::Tools::Run::PiseApplication::checktrans

SYNOPSIS

#

DESCRIPTION

Bio::Tools::Run::PiseApplication::checktrans

      Bioperl class for:

	CHECKTRANS	Reports STOP codons and ORF statistics of a protein (EMBOSS)


      Parameters: 

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


		checktrans (String)

		init (String)

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

		orfml (Integer)
			Minimum ORF Length to report (-orfml)

		report (OutFile)
			report (-report)

		outseq (OutFile)
			Sequence file to hold output ORF sequences (-outseq)
			pipe: seqsfile

		outseq_sformat (Excl)
			Output format for: Sequence file to hold output ORF sequences

		featout (OutFile)
			Feature file for output (-featout)

		featout_offormat (Excl)
			Feature output format (-offormat)

		addlast (Switch)
			Force the sequence to end with an asterisk (-addlast)

		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/checktrans.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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