WSTester updated to work plus hopefully all the other changes that need to go into...

[jabaws.git] / binaries / src / ViennaRNA / interfaces / Perl / RNAfold.pl

diff --git a/binaries/src/ViennaRNA/interfaces/Perl/RNAfold.pl b/binaries/src/ViennaRNA/interfaces/Perl/RNAfold.pl
new file mode 100644 (file)
index 0000000..58d6010
--- /dev/null
+++ b/binaries/src/ViennaRNA/interfaces/Perl/RNAfold.pl
@@ -0,0 +1,144 @@
+#!/usr/bin/perl
+# -*-Perl-*-
+# Last changed Time-stamp: <2006-04-04 14:51:06 ivo>
+
+# Perl implementation of RNAfold
+# This is an example script demonstrating how to use the RNA Perl module
+
+use RNA;
+use Getopt::Long;
+use strict;
+use warnings;
+
+ Getopt::Long::config("no_ignore_case");
+
+use vars qw/$opt_debug $opt_v $ParamFile $pf $ns_bases/;
+my $sfact=1.07;
+&usage() unless GetOptions("p|p1" => \$pf,
+                          "p0" => sub {$pf=1; $RNA::do_backtrack=0},
+                          "C"   => \$RNA::fold_constrained,
+                          "T=f" => \$RNA::temperature,
+                          "4" => sub {$RNA::tetra_loop = 0},
+                          "d|d0" => sub {$RNA::dangles=0},
+                          "d2" => sub {$RNA::dangles=2},,
+                          "noGU" => \$RNA::noGU,
+                          "noCloseGU" => \$RNA::no_closingGU,
+                          "noLP" => \$RNA::noLonelyPairs,
+                          "e=i" => \$RNA::energy_set,
+                          "P=s" => \$ParamFile,
+                          "nsp=s" => \$ns_bases,
+                          "S=f" => \$sfact);
+
+ RNA::read_parameter_file($ParamFile) if ($ParamFile);
+
+if ($ns_bases) {
+   $RNA::nonstandards = "";
+   foreach my $p ( split(/,/, $ns_bases) ) {
+       if ($p =~ s/^-//) {
+           $RNA::nonstandards .= reverse($p)
+           }
+       $RNA::nonstandards .= $p;
+    }
+    print "$RNA::nonstandards\n";
+}
+
+my $istty = (-t STDIN) && (-t STDOUT);
+if (($RNA::fold_constrained)&&($istty)) {
+print <<END
+Input constraints using the following notation:
+ | : paired with another base
+ . : no constraint at all
+ x : base must not pair
+ < : base i is paired with a base j<i
+ > : base i is paired with a base j>i
+matching brackets ( ): base i pairs base j
+END
+}
+
+if ($istty) {
+   print "\nInput string (upper or lower case); @ to quit\n";
+   for (1..8) { print "....,....$_";}
+   print "\n";
+}
+my $fname;
+while (<>) {   # main loop: continue until end of file
+   my ($string, $cstruc, $structure, $min_en);
+   # skip comment lines and get filenames
+   if (/^>\s*(\S*)/) {
+      $fname = $1;
+      next;
+   }
+   last if (/^@/);
+
+   if (/(\S+)/) {
+      $string = $1;
+   } else {
+      next;
+   }
+
+   $string = uc($string);
+   my $length = length($string);
+   printf("length = %d\n", $length) if ($istty);
+
+   if ($RNA::fold_constrained) {
+      $_ = <>;
+      $cstruc = $1 if (/(\S+)/);
+      die("constraint string has wrong length")
+         if (length($cstruc)!=$length);
+      ($structure, $min_en) = RNA::fold($string, $structure);
+   } else {
+     ($structure, $min_en) = RNA::fold($string);
+   }
+   print "$string\n$structure";
+   if ($istty) {
+      printf("\n minimum free energy = %6.2f kcal/mol\n", $min_en);
+   } else {
+      printf(" (%6.2f)\n", $min_en);
+   }
+   my $ffname = ($fname) ? ($fname . '_ss.ps') : 'rna.ps';
+   RNA::PS_rna_plot($string, $structure, $ffname);
+
+   if ($pf) {
+
+      # recompute with dangles as in pf_fold()
+      $RNA::dangles=2 if ($RNA::dangles);
+      $min_en = RNA::energy_of_struct($string, $structure);
+
+      my $kT = ($RNA::temperature+273.15)*1.98717/1000.; # in Kcal
+      $RNA::pf_scale = exp(-($sfact*$min_en)/$kT/$length);
+      print STDERR "scaling factor $RNA::pf_scale\n" if ($length>2000);
+
+      $structure = $cstruc if ($RNA::fold_constrained);
+      my $energy = RNA::pf_fold($string, $structure);
+
+      if ($RNA::do_backtrack) {
+        print $structure;
+        printf(" [%6.2f]\n", $energy) if (!$istty);
+        print "\n";
+      }
+      if (($istty)||(!$RNA::do_backtrack)) {
+        printf(" free energy of ensemble = %6.2f kcal/mol\n", $energy);
+        printf(" frequency of mfe structure in ensemble %g\n",
+               exp(($energy-$min_en)/$kT));
+      }
+
+      if ($RNA::do_backtrack) {
+        $ffname = ($fname)?($fname . "_dp.ps"):"dot.ps";
+        &RNA::PS_dot_plot($string, $ffname);
+      }
+   }
+   undef $fname;
+}
+
+ RNA::free_pf_arrays() if ($pf);
+ RNA::free_arrays();
+
+sub usage()
+{
+   die("usage: " .
+       "RNAfold [-p[0]] [-C] [-T temp] [-4] [-d] [-noGU] [-noCloseGU]\n" .
+       "               [-e e_set] [-P paramfile] [-nsp pairs] [-S scale]");
+}
+
+
+# End of file