SeanMcGrath · April 8, 2015 14:16 · Apr 8, 2015
diff --git a/matrixRMS b/matrixRMS
@@ -0,0 +1,51 @@
+#!/usr/bin/env python
+
+import argparse, sys, csv, math
+
+def calcRMS(reader1, reader2):
+
+    def makeList(reader):
+        l = []
+        for row in reader:
+            for val in row:
+                if val != '':
+                    l.append(float(val.strip()))
+        return l
+
+    dist1 = makeList(reader1)
+    dist2 = makeList(reader2)
+
+    if len(dist1) != len(dist2):
+        return 'File dimensions are incompatible'
+
+    else:
+        gen = zip([el for el in dist1], [el for el in dist2])
+        diffs = [a - b for a, b in gen]
+        squares = [a*a for a in diffs]
+        return math.sqrt(sum(squares)/len(squares))
+
+
+def main(args):
+    parser = argparse.ArgumentParser(description = 'Calculate the RMS deviation of one Gaussian distance matrix from another.')
+    parser.add_argument('File1', type=str)
+    parser.add_argument('File2', type=str)
+
+    args = parser.parse_args(args)
+
+    try:
+        file1 = open(args.File1, 'r')
+        file1reader = csv.reader(file1)
+    except:
+        print('{} is not a valid file'.format(file1))
+        return 2
+    try:
+        file2 = open(args.File2, 'r')
+        file2reader = csv.reader(file2)
+    except:
+        print('{} is not a valid file'.format(file2))
+        return 2
+
+    print(calcRMS(file1reader,file2reader))
+
+if __name__ == '__main__':
+    sys.exit(main(sys.argv[1:]))
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