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Faster grepping 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1948 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2009-10-30 16:59:17 +00:00
parent 4319ff0610
commit 7654051aee
1 changed files with 3 additions and 2 deletions
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5
python/expandedSummaryToGeli.py
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@ -13,7 +13,8 @@ def grep(string, list):
return [elem for elem in list if expr.match(elem)] return [elem for elem in list if expr.match(elem)]
callFile = open(sys.argv[1]) callFile = open(sys.argv[1])
pileupFileName = sys.argv[2] pileupFileLines = open(sys.argv[2])
pileupFileLines = pileupFileLines.readlines()
for line in callFile: for line in callFile:
# note: file is a .csv; so comma delimited with headers # note: file is a .csv; so comma delimited with headers
@ -43,7 +44,7 @@ for line in callFile:
g = chrompos.split(":"); g = chrompos.split(":");
chrompos = g.pop(0)+" "+g.pop(0) chrompos = g.pop(0)+" "+g.pop(0)
#print(chrompos) #print(chrompos)
pileupLine = grepFile(chrompos,open(pileupFileName)) pileupLine = grep(chrompos,pileupFileLines)
#print(pileupLine) #print(pileupLine)
# line is # line is
# chr pos ref num_A num_C num_G num_T # chr pos ref num_A num_C num_G num_T