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Skip entries in genotype matrix that are not in filtered genotype pos… #4

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Skip entries in genotype matrix that are not in filtered genotype pos… #4

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3 changes: 3 additions & 0 deletions eigenMT.py
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Original file line number Diff line number Diff line change
Expand Up @@ -74,6 +74,9 @@ def make_gen_dict(GEN_fh, pos_dict):

for line in GEN: #Go through each line of the genotype matrix and add line to gen_dict
line = line.rstrip().split()
if line[0] not in pos_dict:
# skip entries in genotype matrix that are not on selected chromosome
continue
snp = pos_dict[line[0]]
genos = np.array(line[1:])
genos[genos == 'NA'] = -1
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