NAME

Bio::Tools::Run::PiseApplication::domainer

SYNOPSIS

#

DESCRIPTION

Bio::Tools::Run::PiseApplication::domainer

      Bioperl class for:

	DOMAINER	Build domain coordinate files (EMBOSS)


      Parameters: 

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


		domainer (String)

		init (String)

		scop (InFile)
			Name of scop file for input (embl-like format) (-scop)

		cpdb (String)
			Location of coordinate files for input (embl-like format) (-cpdb)

		cpdbscop (String)
			Location of coordinate files for output (embl-like format) (-cpdbscop)

		cpdbextn (String)
			Extension of coordinate files (embl-like format) (-cpdbextn)

		pdbscop (String)
			Location of coordinate files for output (pdb format) (-pdbscop)

		pdbextn (String)
			Extension of coordinate files (pdb format) (-pdbextn)

		cpdberrf (OutFile)
			Name of log file for the embl-like format build (-cpdberrf)

		pdberrf (OutFile)
			Name of log file for the pdb format build (-pdberrf)

		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/domainer.html

• Bio::Tools::Run::PiseApplication

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

• Bio::Tools::Run::PiseJob

new

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