Mercurial > repos > gregory-minevich > ems_variant_density_mapping

changeset 4:d2158e476320 draft

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Uploaded
author gregory-minevich
date Thu, 14 Jun 2012 21:22:09 -0400
parents 2e236e914815
children d3486ca6b8f4
files EMS_VariantDensityMapping.py
diffstat 1 files changed, 5 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- 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]