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

[jabaws.git] / binaries / src / ViennaRNA / Utils / b2mt.pl

diff --git a/binaries/src/ViennaRNA/Utils/b2mt.pl b/binaries/src/ViennaRNA/Utils/b2mt.pl
new file mode 100644 (file)
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+++ b/binaries/src/ViennaRNA/Utils/b2mt.pl
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+#!/usr/bin/perl -w
+# -*-Perl-*-
+# Last changed Time-stamp: <2005-03-09 19:38:25 ivo> 
+# produce Pauline's mountain representation from bracket notation
+# use e.g. as  RNAfold < foo.seq | b2mt | xmgr -pipe
+# definition: h=number of base pairs enclosing base
+use strict;
+while (<>) {
+    print if (s/>/#/);
+
+    next unless (/\.\.\./);
+    next if (/\[/);   # don't process output from partition function
+    chop;
+    my @F=split(//,$_);
+    my $p=0; my $h=0;
+    foreach my $i (@F) {
+       $h-- if ($i eq ')');
+       $p++;
+       printf("%4d %4d\n",$p,$h);
+       $h++ if ($i eq '(');    # increase $h *after* printing
+    }
+    print "&\n";
+}
+
+=head1 NAME
+
+b2mt - produce coordinates for a mountain plot from bracket notation
+
+=head1 SYNOPSIS
+
+  b2mt.pl < seq.fold > mountain.dat
+
+=head1 DESCRIPTION
+
+read a secondary structures in bracket notation as output by RNAfold,
+and compute coordinates for a mountain plot as introduced by Pauline Hogeweg.
+The output is suitable for graphing  with xmgrace, e.g.:
+C< RNAfold < foo.seq | b2mt.pl | xmgrace -pipe>
+
+=head1 AUTHOR
+
+Ivo L. Hofacker <ivo@tbi.univie.ac.at>