#!/opt/conda/conda-bld/viennarna_1608131744412/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/bin/perl

use strict;
use warnings;
use Getopt::Long qw( :config posix_default bundling no_ignore_case );
use Pod::Usage;
use RNA::Design;

# ********************** #
# Initialize RNA::Design #
# ...................... #
my $ViennaDesign = RNA::Design->new();

# ******************* #
# Get Input Arguments #
# ................... #

my @structs;
my $constr;
my $length = 0;
my $cutpnt = -1;
my $findpath = 10;

# These are also the defaults in RNA::Design.pm
my $optfun = 'eos(1)+eos(2)-2*efe() + 0.3*(eos(1)-eos(2)+0.00)**2';
my $scores = ({AAAAA => 5, CCCCC => 5, GGGGG => 5, UUUUU => 5});
my $bprobs = ({A => 0.25, C => 0.25, G => 0.25, U => 0.25});
my $bpenal = 500;

my ($n, $m) = (1, 1e10);
my $startseq =undef;
my $ParamFile=undef;
my $verbose = 0;
my $jango = 0;

GetOptions(
  # ViennaDesign parameters
  "o|optfun=s"  => sub{$optfun = check_input_costfunction($_[1])},
  "a|avoid=s"   => sub{$scores = check_input_avoid($_[1])},
  "p|bprobs=s"  => sub{($bprobs,$bpenal) = check_input_base_probs($_[1], $bpenal)},
  "n|number=i"  => \$n, # number of independent runs
  "m|maxiter=i" => \$m, # maximal number of steps
  "findpath=i"  => \$findpath,
  "s|start=s"   => \$startseq,

  # ViennaRNA energy parameters
  "P|params=s"  => \$ParamFile,
  "4|tetloops"  => sub {$RNA::tetra_loop=0},
  "d|dangle=i"  => sub {$RNA::dangles=$_[1]},
  "noGU"        => \$RNA::noGU,
  "noCloseGU"   => \$RNA::no_closingGU,

  # other
  "v|verbose=i" => \$verbose,
  "j|jango=i"   => \$jango,

  "h|help"      => sub{pod2usage(1)},
  "man"         => sub{pod2usage(-exitstatus => 1, -verbose => 2)},
) or pod2usage(1);

read_input(\@structs, \$constr, \$length, \$cutpnt);

--$length if $cutpnt != -1;
$constr = 'N' x $length unless $constr;

# ******************* #
# Set Input Arguments #
# ................... #
$ViennaDesign->set_cut_point($cutpnt);
$ViennaDesign->set_structures(@structs);
$ViennaDesign->set_constraint($constr);
$ViennaDesign->set_optfunc($optfun);
$ViennaDesign->set_base_probs($bprobs);
$ViennaDesign->set_base_penalty($bpenal);
$ViennaDesign->set_score_motifs($scores);
$ViennaDesign->set_findpath_bound($findpath);
RNA::read_parameter_file($ParamFile) if ($ParamFile);
#alternative: $ViennaDesign->set_parameter_file($ParamFile) if $ParamFile;

if ($verbose) {
  print "Option-check:\n";
  print "Score: $_ = $$scores{$_}\n" foreach keys %$scores;
  print "Base-prob $_ = $$bprobs{$_}\n" foreach keys %$bprobs;
  print "Base-penalty $bpenal\n";
  print "Objective Function: ".$ViennaDesign->get_optfunc."\n";
  $ViennaDesign->set_verbosity($verbose);
}

# ******************* #
# Design Preparations #
# ................... #

$ViennaDesign->find_dependency_paths;
$ViennaDesign->explore_sequence_space;
#$ViennaDesign->eval_sequence($ViennaDesign->find_a_sequence);

# **************** #
# Main Design Loop #
# ................ #

my %final;
my ($seq, $cost, $count);
for (1 .. $n) {

  # Jango-Method: 
  if ($jango) {
    warn "Jango with $jango presamples\n";
    die "Conflicting Options (--jango & --start)" if $_==1 && $startseq;
    $startseq = $ViennaDesign->find_a_sequence;
    for (my $c=0; $c<$jango; ++$c) {
      my $tmpseq = $ViennaDesign->find_a_sequence;
      if ($ViennaDesign->eval_sequence($tmpseq) < $ViennaDesign->eval_sequence($startseq)) {
        $startseq = $tmpseq;
      }
    }
  }

  $seq = ($startseq) ? $startseq : $ViennaDesign->find_a_sequence;
  $seq = $ViennaDesign->optimize_sequence($seq, $m);

  if (exists $final{$seq}) {
    $cost = $final{$seq}[0];
    $final{$seq}[1]++;
  } else {
    $cost = $ViennaDesign->eval_sequence($seq);
    $final{$seq}[0] = $cost;
    $final{$seq}[1]++;
  }
}

# ************* #
# Print Results #
# ............. #

my $id=1;
foreach $seq (sort {$final{$a}[0]<=>$final{$b}[0]} keys %final) {
  my $cseq = $seq;
  substr $cseq, $cutpnt-1,0,'&' if ($ViennaDesign->get_cut_point != -1);
  printf "%3d %s %6.2f %d\n", $id++, $cseq, $final{$seq}[0], $final{$seq}[1];
}

#############################

sub read_input {
  my ($str,$con,$len,$cut) = @_;

  while (<>) {
    chomp;
    next if $_ eq '';

    # Check if length is consistent
    # TODO treat sequeces with '$' different to allow for cotranscr
    $$len = length $_ unless $$len;
    if (length $_ != $$len) {
      die "All structures/constraints must have the same length!";
    }

    # Set cut-point
    my $tmp = index $_, '&';
    if ($tmp != -1 || $$cut != -1) { # it is a cofold-design!
      ++$tmp;
      if ($$cut == -1) {
        $$cut = $tmp;
      } elsif ($tmp != $$cut) {
        die "cut_points ('&') may not differ in input";
      }
      s/&//; 
      die "only one cut_point ('&') allowed" if s/&//;
    }

    if (m/[\(\)\.x\&]/g) { # is a structure constraint!
      if (m/[^\(\)\.\&x]/g) { # only valid characters!
        die "$_ contains forbidden character: $&";
      } 
      push @$str, $_;
    } elsif (m/[ACUGTURYSMWKVHDBN]/) { # is a sequence constraint!
      if (m/[^ACUGTURYSMWKVHDBN&]/g) { # only valid characters!
        die "Constraint contains a non-iupack caracter: $&";
      }
      die "Only one constraint allowed!" if ($$con);
      $$con = $_;
    }
  }
  return 1;
}

sub check_input_costfunction {
  # TODO: need to check this in a better way!
  # TODO: check for large integers (especially in **2)
  my $optfun = shift;

  # TODO: remove these lines once the web is up-to-date
  $optfun =~ s/gfe/efe/g;
  $optfun =~ s/pfc/efe/g;

  my @allowed = qw( + - / * . );
  foreach my $f1 (@allowed) {
    foreach my $f2 (@allowed) {
      my $forbidden = $f1.$f2;
      if ($forbidden eq '**') {
        die "'***' not allowed in objective function" if (index($optfun, '***') != -1);
      } else {
        die "\'$forbidden\' not allowed in objective function" if (index($optfun, $forbidden) != -1);
      }
    }
  }
  my $nakedfun = $optfun;
  foreach my $fb ('eos', 'efe', 'prob', '_circ', 'barr', 'acc') {
    $nakedfun =~ s/$fb//g;
  }
  die "cannot interpret \'$&\' in objective function" if ($nakedfun =~ m/[^\-\+\/\(\)\.\*\d\,\s]+/g);
  die "unbalanced brackets in optimization function" if scalar($nakedfun =~ tr/\(//) != scalar($nakedfun =~ tr/\)//);

  return $optfun;
}

sub check_input_avoid {
  my $input = shift;
  my %motifs;

  foreach my $a (split ',', $input) {
    my @tmp = (split ':', $a);
    $motifs{$tmp[0]}=$tmp[1];
  }

  foreach my $a (keys %motifs) {
    $a = uc($a);
    die "String $a in 'avoid' list may only contain A,C,U/T or G" if $a =~ m/[^ACUGT]/g;
    die "Scoring the motif $a with 0 does not make sense!" if $motifs{$a} == 0;
  }

  return (%motifs) ? \%motifs: undef;
}

sub check_input_base_probs {
  my ($input, $penalty) = shift;
  my %bprobs;

  foreach my $a (split ',', $input) {
    my @tmp = (split ':', $a);
    if ($tmp[0] eq 'k') {
      $penalty = $tmp[1];
    } else {
      $bprobs{$tmp[0]}=$tmp[1];
    }
  }

  if (%bprobs) {
    my $tot=0;
    foreach my $b (sort keys %bprobs) {
      die "cannot interpret base: $_ in baseprobabilties" if $b =~ m/[^ACUG]/g || length $b > 1;
      die "bad probability for $b: $bprobs{$b}!" unless $bprobs{$b} =~ m/^\d*\.?\d+$/g;
      $tot+=$bprobs{$b};
    }
    die "Base probabilities must sum up to 1. Currently: $tot\n" if ($tot < 0.98 || $tot > 1.02);
  }
  return \%bprobs, $penalty;
}

__END__

=head1 NAME

RNAdesign.pl - Flexible design of multi-stable RNA molecules

=head1 SYNOPSIS

RNAdesign.pl [-o, --options] < constraints.in

=head1 DESCRIPTION

Conformational design an RNA (or DNA) molecules. An initially random sequence is
iteratively mutated and evaluated according to an objective function (see
Option: B<--optfun>). Whenever a better scoring sequence has been found, the
mutation is accepted, the algorithm terminates once a local minimum is found.

For algorithmic details as well as for choosing an objective function see Stefan
Badelt, "Control of RNA function by conformational design", PhD Thesis (2016).

The input file contains (one or more) secondary structures followed by one
(optional) sequence constraint in I<IUPAC> code (i.e. A, C, G, U/T, N, R, Y, S,
M, W, K, V, H, D, B). Both sequence and structure constraints are strictly
enforced during the design process. However, B<RNAdesign.pl> avoids difficulties
of multi-stable designs where a single nucleotide has more than two dependencies.
In that case, base-pair constraints are not strictly enforced, but still
evaluated in the objective function. A warning will be printed to *STDERR*.

  Input example:
  ((((....((((...))))...))))
  ((((....))))...((((...))))
  NNNNGNRANNNNNNNNNNNNNNAUGN

Secondary structures must be specified with a well-balanced dot-bracket string.
They may contain the following special characters: B<'&'> connects two
sequences to design a pair of interacting RNAs, B<'x'> when a structure is used
in the objective function to compute the accessibility of nucleotides (i. e.
the probability of being unpaired).

=head1 PREREQUISTES

This script is part of the B<ViennaRNA package>. It requires the B<RNA::Design> Perl
library, which has been introduced in B<ViennaRNA package-v2.2>.

=head1 WEB

A web interface to call this script is available at

  http://rna.tbi.univie.ac.at/rnadesign

=head1 CITE

For Details on the Algorithms see

  Badelt S., "Control of RNA function by conformational design", PhD Thesis (2016)

  Flamm C., et al. "Design of Multi-Stable RNA Molecules", RNA 7:254-265 (2001)

=head1 OPTIONS

=over 4

=item B<-o, --optfun> <string>

The objective function is a simplified interface to access functions of the
B<ViennaRNA package>. Every input secondary structure *can* serve as full
target conformation or structure constraint. The objective function can include
terms to compute the free energy of a target structure, the (constrained)
ensemble free energy, the (conditional) probabilities of secondary structure
elements, the accessibility of subsequences and the direct-path barriers
between two structures. All of these terms exist for linear, circular, and
cofolded molecules, as well as for custom specified temperatures. In the
following examples, the indices B<i, j> correspond to the secondary structures
specified in the input file, B<t> is optional to specify the temperature in
Celsius. By default, computations use the standard temperature of 37C.

  eos(i,t): Free energy of structure i at temperature t. [circular: eos_circ(i,t)]

  efe(i,t): Free energy of a constrained secondary structure ensemble. Omitting
  i, or specifying i=0 computes the unconstraint ensemble free energy.
  [circular: efe_circ(i,t)]

  prob(i,j,t): Probability of structure i given structure j. The probability is
  computed from the equilibrium partition functions: Pr(i|j)=Z_i/Z_j. Hence, the
  constraint i *must* include the constraint of j (Pr(i|j)=Z_i+j/Z_j). Omitting
  j, or specifying j=0 computes the probability of i in the unconstrained
  ensemble Pr(i)=Z_i/Z. [circular: prob_circ(i,j,t)]

  acc(i,j,t): Accessibility of an RNA/DNA motif. This function is exactly the
  same as prob(i,j,t), however, it is ment to be used with constraints that use
  the character 'x' to specify strictly unpaired regions. [circular: acc_circ(i,j,t)]

  barr(i,j,t): direct path energy barrier from i to j computed using findpath.
  [circular: not implemented]

By default, two independent penalties are added to the objective function, see
options B<--avoid> and B<--bprobs>. 

Default: I<'eos(1)+eos(2)-2*efe()+0.3*(eos(1)-eos(2)+0.00)**2'>

=item B<-a, --avoid> <string>

A set of sequence motifs that receive an extra penalty. Whenever one of these
motifs is found in a sequence, its penalty is added to the score of the
objective function. Specify pairs of B<motif:penalty> as a comma-separated
string. It is allowed to give certain motifs a negative contribution in order
to favor them during the optimization.

Default: I<AAAAA:5,CCCCC:5,GGGGG:5,UUUUU:5>

=item B<-p, --bprobs> <string>

Set a target distribution of nucleotides in the designed sequence. Whenever the
observed nucleotide content differs from target values, a penalty is added to the
objective function (see B<--optfun>). Let B<p> be a vector of specified base
probabilities and B<q> a vector of observed nucleotide percentages, then the
similarity of these vectors is computed as B<s=sum_n(sqrt(p_n*q_n))> where B<n>
is the index for B<A,C,G,U>. The penalty is calculated B<(1-s)*k>. Specify
base probabilities as a comma-separated string of <base>:<prob> tuples.

Default: I<A:0.25,C:0.25,G:0.25,U:0.25,k:500>

=item B<-n, --number> <int>

Specify the number of independent sequence designs. Default: B<1>

=item B<-m, --maxiter> <int>

Maximum number of trial/error improvements during adaptive walk. The default is
B<1e10>, however, this threshold is only important for large sequence designs,
as the value is calculated automatically form the number of possible sequence
mutations. 

=item B<-s, --start> <string>

Specify a starting sequence for adaptive optimization.

=item B<--findpath> <int>

Specify an upper bound for the 'findpath' direct path search used in the
objective function: B<barr(i,j,t)>. Default B<10>.

=item B<-P, --params> <path-to-file>

Specify a Parameter file other than B<rna_turner2004>. Alternative DNA and RNA
parameter files are distributed with the B<ViennaRNA package>.

=item B<-4, --tetloops> <flag>

Turn off parameters for particular tetra-loop hairpin motifs.

=item B<-d, --dangle> <int [0,1,2,3]>

ViennaRNA dangling energy model. Default: 2

=item B<--noGU> <flag>

Turn off energies for GU base-pairs. 

=item B<--noCloseGU> <flag>

Turn off energies for GU base-pairs at the end of helices.

=item B<-v, --verbose> <int>

Print settings and report every sequence accepted during the adaptive walk.

=item B<-h, --help>

Print short help

=item B<--man>

Show the manual page

=back

=head1 AUTHOR

Stefan Badelt E<lt>stef@tbi.univie.ac.atE<gt>

=head1 VERSION-LOG

  1.00 -- initial release (March, 8th 1016)

=cut

