Comute Catalan Numbers

cat.py

@@ -0,0 +1,34 @@
+#    Copyright (C) 2017 Greenweaves Software Pty Ltd
+#
+#    This is free software: you can redistribute it and/or modify
+#    it under the terms of the GNU General Public License as published by
+#    the Free Software Foundation, either version 3 of the License, or
+#    (at your option) any later version.
+#
+#    This software is distributed in the hope that it will be useful,
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#    GNU General Public License for more details.
+#
+#    You should have received a copy of the GNU General Public License
+#    along with GNU Emacs.  If not, see <http://www.gnu.org/licenses/>
+#
+#    cat 	Catalan Numbers and RNA Secondary Structures 
+
+from rosalind import RosalindException,verify_counts_complete_graph
+
+def CatalanNumbers(N):
+    cn=[1]
+    def helper(n):
+        while len(cn)<n+1:
+            cn.append(sum([cn[k-1]*cn[n-k] for k in range(1,n+1)]))
+    for n in range(0,N+1):
+        helper(n)
+    return cn
+
+def CountNonCrossingMatches(string):
+    counts=verify_counts_complete_graph(string)
+
+if __name__=='__main__':
+    #print (CountNonCrossingMatches('AUAU'))
+    print (CatalanNumbers(12))

pmch.py

@@ -15,22 +15,11 @@
 #
 #    pmch 	Perfect Matchings and RNA Secondary Structures 
 
-from rosalind import RosalindException
+from rosalind import RosalindException,factorial,verify_counts_complete_graph
 def NumberPerfectMatchings(string):
-    def factorial(n):
-        return n*factorial(n-1) if n>1 else 1
-    counts={
-        'A':0,
-        'U':0,
-        'C':0,
-        'G':0
-    }
-    for c in string:
-        counts[c]+=1
-    if counts['A']==counts['U'] and counts['C']==counts['G']:
-        return factorial(counts['A'])*factorial(counts['G'])
-    else:
-        raise RosalindException('Mismatched counts {0}/{1} or {2}/{3}'.format(counts['A'],counts['U'],counts['C'],counts['G']))
-
+
+    counts=verify_counts_complete_graph(string)
+    return factorial(counts['A'])*factorial(counts['G'])
+
 if __name__=='__main__':
     print (NumberPerfectMatchings('CGCUUGCAGGACAAGGUGCAUAUCUUCACCAUCAGCUAAACGAUAGCCGCUCACGCGGGAUGGUGCGUUCCGUG'))

rosalind.py

@@ -277,4 +277,21 @@ class RosalindException(Exception):
     '''
     Provide a common class for all exceptions thrown by the library
     '''
-    pass
+    pass
+
+def factorial(n):
+    return n*factorial(n-1) if n>1 else 1
+
+def verify_counts_complete_graph(string):
+    counts={
+        'A':0,
+        'U':0,
+        'C':0,
+        'G':0
+    }
+    for c in string:
+        counts[c]+=1
+    if counts['A']==counts['U'] and counts['C']==counts['G']:
+        return counts
+    else:
+        raise RosalindException('Mismatched counts {0}/{1} or {2}/{3}'.format(counts['A'],counts['U'],counts['C'],counts['G']))