--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cor.py	Mon Jul 28 11:55:23 2014 -0400
@@ -0,0 +1,88 @@
+#!/usr/bin/env python
+#Greg Von Kuster
+"""
+Calculate correlations between numeric columns in a tab delim file.
+usage: %prog infile output.txt columns method
+"""
+
+import sys
+from rpy import *
+
+def stop_err(msg):
+    sys.stderr.write(msg)
+    sys.exit()
+    
+def main():
+    method = sys.argv[4]
+    assert method in ( "pearson", "kendall", "spearman" )
+
+    try:
+        columns = map( int, sys.argv[3].split( ',' ) )
+    except:
+        stop_err( "Problem determining columns, perhaps your query does not contain a column of numerical data." )
+    
+    matrix = []
+    skipped_lines = 0
+    first_invalid_line = 0
+    invalid_value = ''
+    invalid_column = 0
+
+    for i, line in enumerate( file( sys.argv[1] ) ):
+        valid = True
+        line = line.rstrip('\n\r')
+
+        if line and not line.startswith( '#' ): 
+            # Extract values and convert to floats
+            row = []
+            for column in columns:
+                column -= 1
+                fields = line.split( "\t" )
+                if len( fields ) <= column:
+                    valid = False
+                else:
+                    val = fields[column]
+                    if val.lower() == "na": 
+                        row.append( float( "nan" ) )
+                    else:
+                        try:
+                            row.append( float( fields[column] ) )
+                        except:
+                            valid = False
+                            skipped_lines += 1
+                            if not first_invalid_line:
+                                first_invalid_line = i+1
+                                invalid_value = fields[column]
+                                invalid_column = column+1
+        else:
+            valid = False
+            skipped_lines += 1
+            if not first_invalid_line:
+                first_invalid_line = i+1
+
+        if valid:
+            matrix.append( row )
+
+    if skipped_lines < i:
+        try:
+            out = open( sys.argv[2], "w" )
+        except:
+            stop_err( "Unable to open output file" )
+
+        # Run correlation
+        try:
+            value = r.cor( array( matrix ), use="pairwise.complete.obs", method=method )
+        except Exception, exc:
+            out.close()
+            stop_err("%s" %str( exc ))
+        for row in value:
+            print >> out, "\t".join( map( str, row ) )
+        out.close()
+
+    if skipped_lines > 0:
+        msg = "..Skipped %d lines starting with line #%d. " %( skipped_lines, first_invalid_line )
+        if invalid_value and invalid_column > 0:
+            msg += "Value '%s' in column %d is not numeric." % ( invalid_value, invalid_column )
+        print msg
+
+if __name__ == "__main__":
+    main()