# HG changeset patch
# User gregory-minevich
# Date 1339723329 14400
# Node ID d2158e476320b6ad81fd9e90724186eefe337448
# Parent  2e236e914815ef19b6e3a4b2c15ee959c2254ccf
Uploaded

diff -r 2e236e914815 -r d2158e476320 EMS_VariantDensityMapping.py
--- a/EMS_VariantDensityMapping.py	Tue Mar 27 11:29:11 2012 -0400
+++ b/EMS_VariantDensityMapping.py	Thu Jun 14 21:22:09 2012 -0400
@@ -1,5 +1,6 @@
 #!/usr/bin/python
 
+import re
 import sys
 import optparse
 import csv
@@ -55,7 +56,10 @@
 	x_position_list = []
 
 	for row in reader:
-		chromosome = row[0]
+		chromosome = row[0].upper()
+		chromosome = re.sub("chr", "", chromosome, flags = re.IGNORECASE)
+		chromosome = re.sub("CHROMOSOME_", "", chromosome, flags = re.IGNORECASE)
+
 		position = row[1]
 		ref_allele = row[3]
 		alt_allele = row[4]