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

[jabaws.git] / binaries / src / ViennaRNA / Utils / ct2b.pl

diff --git a/binaries/src/ViennaRNA/Utils/ct2b.pl b/binaries/src/ViennaRNA/Utils/ct2b.pl
new file mode 100644 (file)
index 0000000..1a5ee53
--- /dev/null
+++ b/binaries/src/ViennaRNA/Utils/ct2b.pl
@@ -0,0 +1,27 @@
+#!/usr/bin/perl
+# -*-Perl-*-
+# Last changed Time-stamp: <1999-09-29 13:24:23 ivo>
+# produce dot bracket notation of an RNA secondary structure from
+# Zuker's .ct file
+
+while (<>) {
+    @F = split;
+    if ((/ = /) && ($#F!=5)) {
+       if (defined($seq)) {
+           print "$seq\n" unless ($seq eq $oldseq);
+           $oldseq = $seq;
+           print "$s ($E)\n";
+       }
+       $E = $F[3];
+       $s = $seq = "";
+       next;
+    }
+    $seq .= $F[1];
+    if ($F[4]==0) {$s .= "."; next}
+    $s .= "(" if ($F[0]<$F[4]);
+    $s .= ")" if ($F[0]>$F[4]);
+}
+print "$seq\n" unless ($seq eq $oldseq);
+print "$s ($E)\n" if defined($s);
+
+# End of file