zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Now looks up and propagates Syzygy's LOD scores into the appropriate field (so variantfiltration can adjust lod scores accurately) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1950 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2009-10-30 21:13:03 +00:00
parent ea8d5c7077
commit 99337df929
1 changed files with 10 additions and 3 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

13
python/expandedSummaryToGeli.py
View File

@ -14,7 +14,9 @@ def grep(string, list):
callFile = open(sys.argv[1]) callFile = open(sys.argv[1])
pileupFileLines = open(sys.argv[2]) pileupFileLines = open(sys.argv[2])
callFileWithLodScores = open(sys.argv[3])
pileupFileLines = pileupFileLines.readlines() pileupFileLines = pileupFileLines.readlines()
lodFileLines = callFileWithLodScores.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
@ -42,9 +44,10 @@ for line in callFile:
#somehow this next line don't work #somehow this next line don't work
#chrompos.replace(":"," ") #chrompos.replace(":"," ")
g = chrompos.split(":"); g = chrompos.split(":");
chrompos = g.pop(0)+" "+g.pop(0) chromposspc = g.pop(0)+" "+g.pop(0)
#print(chrompos) #print(chrompos)
pileupLine = grep(chrompos,pileupFileLines) pileupLine = grep(chromposspc,pileupFileLines)
lodLine = grep(chrompos,lodFileLines)
#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
@ -60,7 +63,11 @@ for line in callFile:
num_G = int(pileupList.pop(2)) num_G = int(pileupList.pop(2))
num_T = int(pileupList.pop(2)) num_T = int(pileupList.pop(2))
depth = num_A+num_C+num_G+num_T depth = num_A+num_C+num_G+num_T
lodLine = lodLine.pop(0)
lodLine = lodLine.split(" ")
# print(lodLine)
lod = max(float(lodLine.pop(21)),float(lodLine.pop(19)))
# output is # output is
# chr pos ref depth mapping call btr btnb AA AC AG AT CC CG CT GG GT TT # chr pos ref depth mapping call btr btnb AA AC AG AT CC CG CT GG GT TT
outStr = chrompos+" "+ref+" "+str(depth)+" 5 "+variant+" -1 -2 -3 -4 -5 -6 -7 -8 -9 -10 -11 -12" outStr = chrompos+" "+ref+" "+str(depth)+" 5 "+variant+" "+str(lod)+" -2 -3 -4 -5 -6 -7 -8 -9 -10 -11 -12"
print(outStr) print(outStr)