From 7654051aee0e8aa70f3b0253d3697b33b381bf94 Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 30 Oct 2009 16:59:17 +0000
Subject: [PATCH] Faster grepping

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1948 348d0f76-0448-11de-a6fe-93d51630548a
---
 python/expandedSummaryToGeli.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/python/expandedSummaryToGeli.py b/python/expandedSummaryToGeli.py
index caa2bced6..b92a74973 100755
--- a/python/expandedSummaryToGeli.py
+++ b/python/expandedSummaryToGeli.py
@@ -13,7 +13,8 @@ def grep(string, list):
     return [elem for elem in list if expr.match(elem)]
 
 callFile = open(sys.argv[1])
-pileupFileName = sys.argv[2]
+pileupFileLines = open(sys.argv[2])
+pileupFileLines = pileupFileLines.readlines()
 
 for line in callFile:
 # note: file is a .csv; so comma delimited with headers
@@ -43,7 +44,7 @@ for line in callFile:
         g = chrompos.split(":");
         chrompos = g.pop(0)+" "+g.pop(0)
         #print(chrompos)
-        pileupLine = grepFile(chrompos,open(pileupFileName))
+        pileupLine = grep(chrompos,pileupFileLines)
         #print(pileupLine)
         # line is
         # chr pos ref num_A num_C num_G num_T