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Fix dataset reading and pearson correlation is 0 #31

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Fix dataset reading and pearson correlation is 0 #31

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269aaa5
Fix reading datasets from base_list if defined without '/' in the names.
ghuls May 28, 2020
d1f5c80
Allow Pearson correlation to be zero.
ghuls May 28, 2020
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6 changes: 4 additions & 2 deletions ncm.py
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Original file line number Diff line number Diff line change
Expand Up @@ -56,7 +56,9 @@ def pearson_def(x, y):
xdiff2 += xdiff * xdiff
ydiff2 += ydiff * ydiff

return diffprod / math.sqrt(xdiff2 * ydiff2)
sqrt_xdiff2_ydiff2 = math.sqrt(xdiff2 * ydiff2)

return diffprod / sqrt_xdiff2_ydiff2 if sqrt_xdiff2_ydiff2 != 0.0 else 0.0

# createDataSet
# base_dir : directory of files, bedFile: name of the bedFile
Expand Down Expand Up @@ -251,7 +253,7 @@ def createDataSetFromList(base_list, bedFile):
link = line.strip()
f = open(link, "r")
dbsnpf= open(bedFile,"r")
file = link[link.rindex("/")+1:]
file = os.path.basename(link)
depth = dict()
depth[file] = 0
real_count[file] = 0
Expand Down