# rnainverse.pm,v 1.3.2.1 2005/10/09 15:19:48 jason Exp
# BioPerl module for Bio::Tools::Run::PiseApplication::rnainverse
#
# Cared for by Catherine Letondal <letondal@pasteur.fr>
#
# For copyright and disclaimer see below.
#
# POD documentation - main docs before the code

=head1 NAME

Bio::Tools::Run::PiseApplication::rnainverse

=head1 SYNOPSIS

  #

=head1 DESCRIPTION

Bio::Tools::Run::PiseApplication::rnainverse

      Bioperl class for:

	VIENNARNA	RNAinverse - find RNA sequences with given secondary structure (Hofacker)

	References:

		I.L. Hofacker, W. Fontana, P.F. Stadler, S. Bonhoeffer, M. Tacker, P. Schuster (1994) Fast Folding and Comparison of RNA Secondary Structures. Monatshefte f. Chemie 125: 167-188

		A. Walter, D Turner, J Kim, M Lyttle, P Muller, D Mathews, M Zuker Coaxial stacking of helices enhances binding of oligoribonucleotides. PNAS, 91, pp 9218-9222, 1994

		M. Zuker, P. Stiegler (1981) Optimal computer folding of large RNA sequences using thermodynamic and auxiliary information, Nucl Acid Res 9: 133-148

		J.S. McCaskill (1990) The equilibrium partition function and base pair binding probabilities for RNA secondary structures, Biopolymers 29: 11051119 D.H. Turner N. Sugimoto and S.M. Freier (1988) RNA structure prediction, Ann Rev Biophys Biophys Chem 17: 167-192

		D. Adams (1979) The hitchhiker's guide to the galaxy, Pan Books, London



      Parameters: 

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


		rnainverse (String)

		seqstruct (InFile)
			Sequences/Structures File

		folding (Excl)
			Folding method (-F)

		final (Integer)
			Stop search when sequence is found with E(s)-F smaller than this value (-f)

		repeats (Integer)
			Search repeatedly for the same structure (-R)

		alphabet (String)
			Find sequences using only bases from this alphabet (-a)

		temperature (Integer)
			Rescale energy parameters to a temperature of temp C. (-T)

		tetraloops (Switch)
			Do not include special stabilizing energies for certain tetraloops (-4)

		dangling (Excl)
			How to treat dangling end energies for bases adjacent to helices in free ends and multiloops (-d)

		noGU (Switch)
			Do not allow GU pairs (-noGU)

		noCloseGU (Switch)
			Do not allow GU pairs at the end of helices (-noCloseGU)

		nsp (String)
			Non standard pairs (comma seperated list) (-nsp)

		parameter (InFile)
			Parameter file (-P)

		energy (Excl)
			Energy parameters for the artificial ABCD... alphabet (-e)

		readseq (String)

=head1 FEEDBACK

=head2 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

=head2 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.bioperl.org/

=head1 AUTHOR

Catherine Letondal (letondal@pasteur.fr)

=head1 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.

=head1 DISCLAIMER

This software is provided "as is" without warranty of any kind.

=head1 SEE ALSO

=over

=item *

http://bioweb.pasteur.fr/seqanal/interfaces/rnainverse.html

=item *

Bio::Tools::Run::PiseApplication

=item *

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

=item *

Bio::Tools::Run::PiseJob

=back

=cut

#'
package Bio::Tools::Run::PiseApplication::rnainverse;

use vars qw(@ISA);
use strict;
use Bio::Tools::Run::PiseApplication;

@ISA = qw(Bio::Tools::Run::PiseApplication);

=head2 new

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

=cut

sub new {
    my ($class, $location, $email, @params) = @_;
    my $self = $class->SUPER::new($location, $email);

# -- begin of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/rnainverse.pm

    $self->{COMMAND}   = "rnainverse";
    $self->{VERSION}   = "5.a";
    $self->{TITLE}   = "VIENNARNA";

    $self->{DESCRIPTION}   = "RNAinverse - find RNA sequences with given secondary structure";

    $self->{OPT_EMAIL}   = 0;

    $self->{AUTHORS}   = "Hofacker";

    $self->{DOCLINK}   = "http://bioweb.pasteur.fr/docs/gensoft-na.html#VIENNARNA";

    $self->{REFERENCE}   = [

         "I.L. Hofacker, W. Fontana, P.F. Stadler, S. Bonhoeffer, M. Tacker, P. Schuster (1994) Fast Folding and Comparison of RNA Secondary Structures. Monatshefte f. Chemie 125: 167-188",

         "A. Walter, D Turner, J Kim, M Lyttle, P Muller, D Mathews, M Zuker Coaxial stacking of helices enhances binding of oligoribonucleotides. PNAS, 91, pp 9218-9222, 1994",

         "M. Zuker, P. Stiegler (1981) Optimal computer folding of large RNA sequences using thermodynamic and auxiliary information, Nucl Acid Res 9: 133-148",

         "J.S. McCaskill (1990) The equilibrium partition function and base pair binding probabilities for RNA secondary structures, Biopolymers 29: 11051119 D.H. Turner N. Sugimoto and S.M. Freier (1988) RNA structure prediction, Ann Rev Biophys Biophys Chem 17: 167-192",

         "D. Adams (1979) The hitchhiker's guide to the galaxy, Pan Books, London",
 ];

    $self->{_INTERFACE_STANDOUT} = undef;
    $self->{_STANDOUT_FILE} = undef;

    $self->{TOP_PARAMETERS}  = [ 
	"rnainverse",
	"seqstruct",
	"control",
	"others_options",
	"readseq",

    ];

    $self->{PARAMETERS_ORDER}  = [
	"rnainverse",
	"seqstruct", 	# Sequences/Structures File
	"control", 	# Control options
	"folding", 	# Folding method (-F)
	"final", 	# Stop search when sequence is found with E(s)-F smaller than this value (-f)
	"repeats", 	# Search repeatedly for the same structure (-R)
	"alphabet", 	# Find sequences using only bases from this alphabet (-a)
	"others_options", 	# Other options
	"temperature", 	# Rescale energy parameters to a temperature of temp C. (-T)
	"tetraloops", 	# Do not include special stabilizing energies for certain tetraloops (-4)
	"dangling", 	# How to treat dangling end energies for bases adjacent to helices in free ends and multiloops (-d)
	"noGU", 	# Do not allow GU pairs (-noGU)
	"noCloseGU", 	# Do not allow GU pairs at the end of helices (-noCloseGU)
	"nsp", 	# Non standard pairs (comma seperated list) (-nsp)
	"parameter", 	# Parameter file (-P)
	"energy", 	# Energy parameters for the artificial ABCD... alphabet (-e)
	"readseq",

    ];

    $self->{TYPE}  = {
	"rnainverse" => 'String',
	"seqstruct" => 'InFile',
	"control" => 'Paragraph',
	"folding" => 'Excl',
	"final" => 'Integer',
	"repeats" => 'Integer',
	"alphabet" => 'String',
	"others_options" => 'Paragraph',
	"temperature" => 'Integer',
	"tetraloops" => 'Switch',
	"dangling" => 'Excl',
	"noGU" => 'Switch',
	"noCloseGU" => 'Switch',
	"nsp" => 'String',
	"parameter" => 'InFile',
	"energy" => 'Excl',
	"readseq" => 'String',

    };

    $self->{FORMAT}  = {
	"rnainverse" => {
		"perl" => '"RNAinverse"',
	},
	"seqstruct" => {
		"perl" => '" < $value" ',
	},
	"control" => {
	},
	"folding" => {
		"perl" => '(defined $value && $value ne $vdef)? " -F$value" : ""',
	},
	"final" => {
		"perl" => '(defined $value)? " -f $value" : ""',
	},
	"repeats" => {
		"perl" => '(defined $value)? " -R $value" : ""',
	},
	"alphabet" => {
		"perl" => '($value)? " -a $value" : ""',
	},
	"others_options" => {
	},
	"temperature" => {
		"perl" => '(defined $value && $value ne $vdef)? " -T $value" : ""',
	},
	"tetraloops" => {
		"perl" => '($value)? " -4" : ""',
	},
	"dangling" => {
		"perl" => '($value)? " $value" : ""',
	},
	"noGU" => {
		"perl" => '($value)? " -noGU" : ""',
	},
	"noCloseGU" => {
		"perl" => '($value)? " -noCloseGU" : ""',
	},
	"nsp" => {
		"perl" => '($value)? " -nsp $value" : "" ',
	},
	"parameter" => {
		"perl" => '($value)? " -P $value" : ""',
	},
	"energy" => {
		"perl" => '($value)? " -e $value" : ""',
	},
	"readseq" => {
		"perl" => '"/local/gensoft/lib/ViennaRNA/readseq  -f=19 -a $seq > $seq.tmp && (cp $seq $seq.orig && mv $seq.tmp $seq) ; "',
	},

    };

    $self->{FILENAMES}  = {

    };

    $self->{SEQFMT}  = {

    };

    $self->{GROUP}  = {
	"rnainverse" => 0,
	"seqstruct" => 1000,
	"control" => 2,
	"folding" => 2,
	"final" => 2,
	"repeats" => 2,
	"alphabet" => 2,
	"others_options" => 2,
	"temperature" => 2,
	"tetraloops" => 2,
	"dangling" => 2,
	"noGU" => 2,
	"noCloseGU" => 2,
	"nsp" => 2,
	"parameter" => 2,
	"energy" => 2,
	"readseq" => -10,

    };

    $self->{BY_GROUP_PARAMETERS}  = [
	"readseq",
	"rnainverse",
	"control",
	"folding",
	"final",
	"repeats",
	"alphabet",
	"others_options",
	"temperature",
	"tetraloops",
	"dangling",
	"noGU",
	"noCloseGU",
	"nsp",
	"parameter",
	"energy",
	"seqstruct",

    ];

    $self->{SIZE}  = {

    };

    $self->{ISHIDDEN}  = {
	"rnainverse" => 1,
	"seqstruct" => 0,
	"control" => 0,
	"folding" => 0,
	"final" => 0,
	"repeats" => 0,
	"alphabet" => 0,
	"others_options" => 0,
	"temperature" => 0,
	"tetraloops" => 0,
	"dangling" => 0,
	"noGU" => 0,
	"noCloseGU" => 0,
	"nsp" => 0,
	"parameter" => 0,
	"energy" => 0,
	"readseq" => 1,

    };

    $self->{ISCOMMAND}  = {
	"rnainverse" => 1,
	"seqstruct" => 0,
	"control" => 0,
	"folding" => 0,
	"final" => 0,
	"repeats" => 0,
	"alphabet" => 0,
	"others_options" => 0,
	"temperature" => 0,
	"tetraloops" => 0,
	"dangling" => 0,
	"noGU" => 0,
	"noCloseGU" => 0,
	"nsp" => 0,
	"parameter" => 0,
	"energy" => 0,
	"readseq" => 0,

    };

    $self->{ISMANDATORY}  = {
	"rnainverse" => 0,
	"seqstruct" => 1,
	"control" => 0,
	"folding" => 0,
	"final" => 0,
	"repeats" => 0,
	"alphabet" => 0,
	"others_options" => 0,
	"temperature" => 0,
	"tetraloops" => 0,
	"dangling" => 0,
	"noGU" => 0,
	"noCloseGU" => 0,
	"nsp" => 0,
	"parameter" => 0,
	"energy" => 0,
	"readseq" => 0,

    };

    $self->{PROMPT}  = {
	"rnainverse" => "",
	"seqstruct" => "Sequences/Structures File",
	"control" => "Control options",
	"folding" => "Folding method (-F)",
	"final" => "Stop search when sequence is found with E(s)-F smaller than this value (-f)",
	"repeats" => "Search repeatedly for the same structure (-R)",
	"alphabet" => "Find sequences using only bases from this alphabet (-a)",
	"others_options" => "Other options",
	"temperature" => "Rescale energy parameters to a temperature of temp C. (-T)",
	"tetraloops" => "Do not include special stabilizing energies for certain tetraloops (-4)",
	"dangling" => "How to treat dangling end energies for bases adjacent to helices in free ends and multiloops (-d)",
	"noGU" => "Do not allow GU pairs (-noGU)",
	"noCloseGU" => "Do not allow GU pairs at the end of helices (-noCloseGU)",
	"nsp" => "Non standard pairs (comma seperated list) (-nsp)",
	"parameter" => "Parameter file (-P)",
	"energy" => "Energy parameters for the artificial ABCD... alphabet (-e)",
	"readseq" => "",

    };

    $self->{ISSTANDOUT}  = {
	"rnainverse" => 0,
	"seqstruct" => 0,
	"control" => 0,
	"folding" => 0,
	"final" => 0,
	"repeats" => 0,
	"alphabet" => 0,
	"others_options" => 0,
	"temperature" => 0,
	"tetraloops" => 0,
	"dangling" => 0,
	"noGU" => 0,
	"noCloseGU" => 0,
	"nsp" => 0,
	"parameter" => 0,
	"energy" => 0,
	"readseq" => 0,

    };

    $self->{VLIST}  = {

	"control" => ['folding','final','repeats','alphabet',],
	"folding" => ['m','m: minimum energy','p','p: partition function','mp','mp: both',],
	"others_options" => ['temperature','tetraloops','dangling','noGU','noCloseGU','nsp','parameter','energy',],
	"dangling" => ['','only unpaired bases can participate in at most one dangling end','-d','-d: ignores dangling ends altogether','-d2','-d2: the check is ignored, this is the default for partition function folding.',],
	"energy" => ['1','1: use energy parameters for GC pairs','2','2: use energy parameters for AU pairs',],
    };

    $self->{FLIST}  = {

    };

    $self->{SEPARATOR}  = {

    };

    $self->{VDEF}  = {
	"rnainverse" => 'rnainverse',
	"folding" => 'm',
	"temperature" => '37',
	"tetraloops" => '0',
	"dangling" => '""',
	"noGU" => '0',
	"noCloseGU" => '0',

    };

    $self->{PRECOND}  = {
	"rnainverse" => { "perl" => '1' },
	"seqstruct" => { "perl" => '1' },
	"control" => { "perl" => '1' },
	"folding" => { "perl" => '1' },
	"final" => {
		"perl" => '$folding =~ /p/',
	},
	"repeats" => { "perl" => '1' },
	"alphabet" => { "perl" => '1' },
	"others_options" => { "perl" => '1' },
	"temperature" => { "perl" => '1' },
	"tetraloops" => { "perl" => '1' },
	"dangling" => { "perl" => '1' },
	"noGU" => { "perl" => '1' },
	"noCloseGU" => { "perl" => '1' },
	"nsp" => { "perl" => '1' },
	"parameter" => { "perl" => '1' },
	"energy" => { "perl" => '1' },
	"readseq" => {
		"perl" => 'defined $rnafold || defined $rnasubopt',
	},

    };

    $self->{CTRL}  = {
	"dangling" => {
		"perl" => {
			'(! (defined $rnafold || defined $rnaeval || defined $rnainverse) &&   ($dangling eq "-d2")  && ($dangling = "") && 0)' => "no message",
		},
	},

    };

    $self->{PIPEOUT}  = {

    };

    $self->{WITHPIPEOUT}  = {

    };

    $self->{PIPEIN}  = {

    };

    $self->{WITHPIPEIN}  = {

    };

    $self->{ISCLEAN}  = {
	"rnainverse" => 0,
	"seqstruct" => 0,
	"control" => 0,
	"folding" => 0,
	"final" => 0,
	"repeats" => 0,
	"alphabet" => 0,
	"others_options" => 0,
	"temperature" => 0,
	"tetraloops" => 0,
	"dangling" => 0,
	"noGU" => 0,
	"noCloseGU" => 0,
	"nsp" => 0,
	"parameter" => 0,
	"energy" => 0,
	"readseq" => 0,

    };

    $self->{ISSIMPLE}  = {
	"rnainverse" => 0,
	"seqstruct" => 1,
	"control" => 0,
	"folding" => 0,
	"final" => 0,
	"repeats" => 0,
	"alphabet" => 0,
	"others_options" => 0,
	"temperature" => 0,
	"tetraloops" => 0,
	"dangling" => 0,
	"noGU" => 0,
	"noCloseGU" => 0,
	"nsp" => 0,
	"parameter" => 0,
	"energy" => 0,
	"readseq" => 0,

    };

    $self->{PARAMFILE}  = {

    };

    $self->{COMMENT}  = {
	"seqstruct" => [
		"Target structures and starting sequences for the search are read alternately from stdin. If a \'0\' is given instead of a starting sequence a random sequence is used.",
	],
	"final" => [
		"In combination with -Fp",
		"F=-kT*ln(Q)",
	],
	"repeats" => [
		"If \'0\' was given instead of a starting sequence, a new random starting sequences is used for each subsequent trial.",
		"If repeats is negative search until -repeats exact solutions are found, no output is done for unsuccessful searches.",
		"The program will not terminate if the target can not be found.",
	],
	"dangling" => [
		"How to treat \'dangling end\' energies for bases adjacent to helices in free ends and multiloops: Normally only unpaired bases can participate in at most one dangling end. With -d2 this check is ignored, this is the default for partition function folding (-p). -d ignores dangling ends altogether. Note that by default pf and mfe folding treat dangling ends differently, use -d2 (or -d) in addition to -p to ensure that both algorithms use the same energy model. The -d2 options is available for RNAfold, RNAeval, and RNAinverse only.",
	],
	"nsp" => [
		"Allow other pairs in addition to the usual AU,GC,and GU pairs. pairs is a comma seperated list of additionally allowed pairs. If a the first character is a \'-\' then AB will imply that AB and BA are allowed pairs. e.g. RNAfold -nsp -GA will allow GA and AG pairs. Nonstandard pairs are given 0 stacking energy.",
	],
	"parameter" => [
		"Read energy parameters from paramfile, instead of using the default parameter set. A sample parameterfile should accompany your distribution. See the RNAlib documentation for details on the file format.",
	],

    };

    $self->{SCALEMIN}  = {

    };

    $self->{SCALEMAX}  = {

    };

    $self->{SCALEINC}  = {

    };

    $self->{INFO}  = {

    };

# -- end of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/rnainverse.pm



    $self->_init_params(@params);

    return $self;
}



1; # Needed to keep compiler happy

