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# $Id: rnaheat.pm,v 1.6 2006/07/04 22:23:35 mauricio Exp $
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# BioPerl module for Bio::Tools::Run::PiseApplication::rnaheat
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# Cared for by Catherine Letondal <letondal@pasteur.fr>
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# For copyright and disclaimer see below.
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# POD documentation - main docs before the code
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Bio::Tools::Run::PiseApplication::rnaheat
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Bio::Tools::Run::PiseApplication::rnaheat
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VIENNARNA RNAheat - calculate specific heat of RNAs (Hofacker, Stadler)
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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
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J.S. McCaskill (1990) The equilibrium partition function and base pair binding probabilities for RNA secondary structures, Biopolymers 29: 11051119 D. Adams (1979) The hitchhiker's guide to the galaxy, Pan Books, London
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http://bioweb.pasteur.fr/seqanal/interfaces/rnaheat.html
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for available values):
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Lowest temperature, default is 0C (-Tmin)
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Highest temperature, default is 100C (-Tmax)
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Calculate partition function every stepsize degrees C. Default is 1C (-h)
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Produces a smoother curve by increasing ipoints (-m)
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Do not include special stabilizing energies for certain tetraloops (-4)
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How to treat dangling end energies for bases adjacent to helices in free ends and multiloops (-d)
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Do not allow GU pairs (-noGU)
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Do not allow GU pairs at the end of helices (-noCloseGU)
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Non standard pairs (comma seperated list) (-nsp)
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Energy parameters for the artificial ABCD... alphabet (-e)
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User feedback is an integral part of the evolution of this and other
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Bioperl modules. Send your comments and suggestions preferably to
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the Bioperl mailing list. Your participation is much appreciated.
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bioperl-l@bioperl.org - General discussion
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http://bioperl.org/wiki/Mailing_lists - About the mailing lists
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Report bugs to the Bioperl bug tracking system to help us keep track
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of the bugs and their resolution. Bug reports can be submitted via the
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http://bugzilla.open-bio.org/
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Catherine Letondal (letondal@pasteur.fr)
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Copyright (C) 2003 Institut Pasteur & Catherine Letondal.
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This module is free software; you can redistribute it and/or modify
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it under the same terms as Perl itself.
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This software is provided "as is" without warranty of any kind.
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http://bioweb.pasteur.fr/seqanal/interfaces/rnaheat.html
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Bio::Tools::Run::PiseApplication
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Bio::Tools::Run::AnalysisFactory::Pise
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Bio::Tools::Run::PiseJob
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package Bio::Tools::Run::PiseApplication::rnaheat;
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use Bio::Tools::Run::PiseApplication;
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@ISA = qw(Bio::Tools::Run::PiseApplication);
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Usage : my $rnaheat = Bio::Tools::Run::PiseApplication::rnaheat->new($location, $email, @params);
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Function: Creates a Bio::Tools::Run::PiseApplication::rnaheat object.
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This method should not be used directly, but rather by
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a Bio::Tools::Run::AnalysisFactory::Pise instance.
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my $factory = Bio::Tools::Run::AnalysisFactory::Pise->new();
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my $rnaheat = $factory->program('rnaheat');
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Returns : An instance of Bio::Tools::Run::PiseApplication::rnaheat.
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my ($class, $location, $email, @params) = @_;
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my $self = $class->SUPER::new($location, $email);
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# -- begin of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/rnaheat.pm
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$self->{COMMAND} = "rnaheat";
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$self->{VERSION} = "5.a";
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$self->{TITLE} = "VIENNARNA";
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$self->{DESCRIPTION} = "RNAheat - calculate specific heat of RNAs";
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$self->{OPT_EMAIL} = 0;
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$self->{AUTHORS} = "Hofacker, Stadler";
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$self->{DOCLINK} = "http://bioweb.pasteur.fr/docs/gensoft-na.html#VIENNARNA";
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$self->{REFERENCE} = [
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"I.L. Hofacker, W. Fontana, P.F. Stadler, S. Bonhoeffer, M. Tacker, P. Schuster (1994) Fast Folding and Comparison of RNA Secondary Structures. Monatshefte f. Chemie 125: 167-188",
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"J.S. McCaskill (1990) The equilibrium partition function and base pair binding probabilities for RNA secondary structures, Biopolymers 29: 11051119 D. Adams (1979) The hitchhiker's guide to the galaxy, Pan Books, London",
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$self->{_INTERFACE_STANDOUT} = undef;
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$self->{_STANDOUT_FILE} = undef;
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$self->{TOP_PARAMETERS} = [
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$self->{PARAMETERS_ORDER} = [
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"seq", # RNA Sequences File
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"control", # Control options
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"temp_min", # Lowest temperature, default is 0C (-Tmin)
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"temp_max", # Highest temperature, default is 100C (-Tmax)
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"stepsize", # Calculate partition function every stepsize degrees C. Default is 1C (-h)
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"ipoints", # Produces a smoother curve by increasing ipoints (-m)
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"tetraloops", # Do not include special stabilizing energies for certain tetraloops (-4)
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"dangling", # How to treat dangling end energies for bases adjacent to helices in free ends and multiloops (-d)
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"input", # Input parameters
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"noGU", # Do not allow GU pairs (-noGU)
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"noCloseGU", # Do not allow GU pairs at the end of helices (-noCloseGU)
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"nsp", # Non standard pairs (comma seperated list) (-nsp)
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"parameter", # Parameter file (-P)
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"energy", # Energy parameters for the artificial ABCD... alphabet (-e)
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"rnaheat" => 'String',
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"control" => 'Paragraph',
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"temp_min" => 'Integer',
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"temp_max" => 'Integer',
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"stepsize" => 'Integer',
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"ipoints" => 'Integer',
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"tetraloops" => 'Switch',
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"dangling" => 'Excl',
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"input" => 'Paragraph',
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"noCloseGU" => 'Switch',
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"parameter" => 'InFile',
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"readseq" => 'String',
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"perl" => '"RNAheat"',
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"perl" => '" < $value" ',
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"perl" => '(defined $value && $value ne $vdef)? " -Tmin $value" : ""',
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"perl" => '(defined $value && $value ne $vdef)? " -Tmax $value" : ""',
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"perl" => '(defined $value && $value ne $vdef)? " -h $value" : ""',
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"perl" => '(defined $value && $value ne $vdef)? " -m $value" : ""',
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"perl" => '($value)? " -4" : ""',
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"perl" => '($value)? " $value" : ""',
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"perl" => '($value)? " -noGU" : ""',
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"perl" => '($value)? " -noCloseGU" : ""',
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"perl" => '($value)? " -nsp $value" : "" ',
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"perl" => '($value)? " -P $value" : ""',
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"perl" => '($value)? " -e $value" : ""',
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"perl" => '"/local/gensoft/lib/ViennaRNA/readseq -f=19 -a $seq > $seq.tmp && (cp $seq $seq.orig && mv $seq.tmp $seq) ; "',
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$self->{FILENAMES} = {
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$self->{BY_GROUP_PARAMETERS} = [
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$self->{ISHIDDEN} = {
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$self->{ISCOMMAND} = {
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$self->{ISMANDATORY} = {
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"seq" => "RNA Sequences File",
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"control" => "Control options",
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"temp_min" => "Lowest temperature, default is 0C (-Tmin)",
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"temp_max" => "Highest temperature, default is 100C (-Tmax)",
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"stepsize" => "Calculate partition function every stepsize degrees C. Default is 1C (-h)",
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"ipoints" => "Produces a smoother curve by increasing ipoints (-m)",
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"tetraloops" => "Do not include special stabilizing energies for certain tetraloops (-4)",
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"dangling" => "How to treat dangling end energies for bases adjacent to helices in free ends and multiloops (-d)",
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"input" => "Input parameters",
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"noGU" => "Do not allow GU pairs (-noGU)",
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"noCloseGU" => "Do not allow GU pairs at the end of helices (-noCloseGU)",
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"nsp" => "Non standard pairs (comma seperated list) (-nsp)",
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"parameter" => "Parameter file (-P)",
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"energy" => "Energy parameters for the artificial ABCD... alphabet (-e)",
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$self->{ISSTANDOUT} = {
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"control" => ['temp_min','temp_max','stepsize','ipoints','tetraloops','dangling',],
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"dangling" => ['','only unpaired bases can participate in at most one dangling end','-d','-d: ignores dangling ends altogether','-d2','-d2: the check is ignored, this is the default for partition function folding.',],
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"input" => ['noGU','noCloseGU','nsp','parameter','energy',],
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"energy" => ['1','1: use energy parameters for GC pairs','2','2: use energy parameters for AU pairs',],
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$self->{SEPARATOR} = {
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"rnaheat" => { "perl" => '1' },
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"seq" => { "perl" => '1' },
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"control" => { "perl" => '1' },
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"temp_min" => { "perl" => '1' },
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"temp_max" => { "perl" => '1' },
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"stepsize" => { "perl" => '1' },
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"ipoints" => { "perl" => '1' },
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"tetraloops" => { "perl" => '1' },
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"dangling" => { "perl" => '1' },
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"input" => { "perl" => '1' },
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"noGU" => { "perl" => '1' },
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"noCloseGU" => { "perl" => '1' },
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"nsp" => { "perl" => '1' },
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"parameter" => { "perl" => '1' },
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"energy" => { "perl" => '1' },
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"perl" => 'defined $rnafold || defined $rnasubopt',
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'(! (defined $rnafold || defined $rnaeval || defined $rnainverse) && ($dangling eq "-d2") && ($dangling = "") && 0)' => "no message",
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$self->{WITHPIPEOUT} = {
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$self->{WITHPIPEIN} = {
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$self->{ISSIMPLE} = {
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$self->{PARAMFILE} = {
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"The program fits a parabola to 2*ipoints+1 data points to calculate 2nd derivatives. Increasing this parameter produces a smoother curve. Default is 2.",
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"How to treat \'dangling end\' energies for bases adjacent to helices in free ends and multiloops: Normally only unpaired bases can participate in at most one dangling end. With -d2 this check is ignored, this is the default for partition function folding (-p). -d ignores dangling ends altogether. Note that by default pf and mfe folding treat dangling ends differently, use -d2 (or -d) in addition to -p to ensure that both algorithms use the same energy model. The -d2 options is available for RNAfold, RNAeval, and RNAinverse only.",
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"Allow other pairs in addition to the usual AU,GC,and GU pairs. pairs is a comma seperated list of additionally allowed pairs. If a the first character is a \'-\' then AB will imply that AB and BA are allowed pairs. e.g. RNAfold -nsp -GA will allow GA and AG pairs. Nonstandard pairs are given 0 stacking energy.",
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"Read energy parameters from paramfile, instead of using the default parameter set. A sample parameterfile should accompany your distribution. See the RNAlib documentation for details on the file format.",
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$self->{SCALEMIN} = {
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$self->{SCALEMAX} = {
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$self->{SCALEINC} = {
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# -- end of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/rnaheat.pm
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$self->_init_params(@params);
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1; # Needed to keep compiler happy
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Bio/Tools/Run/PiseApplication/rnaheat.pm
