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fix issue #11 - specify vm polarity column; handle dm empty upper left hand cell #12

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fix issue #11 - specify vm polarity column; handle dm empty upper left hand cell #12

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b539d66
handle custom polarity column and data matrix upper left hand column
eschen42 Jun 9, 2021
2eba095
use column 2 if polarity is not specified in the header
eschen42 Jun 9, 2021
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11 changes: 9 additions & 2 deletions vkmz/read.py
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Original file line number Diff line number Diff line change
Expand Up @@ -230,13 +230,17 @@ def xcmsTabular(sample_file, variable_file, matrix_file):
polarity = {}
with open(sample_file, "r") as f:
sample_data = csv.reader(f, delimiter="\t")
next(sample_data) # skip header
header = next(sample_data) # skip header
if 'polarity' in header:
polarity_index = header.index("polarity")
else:
polarity_index = 2
for row in sample_data:
sample = row[0]
if POLARITY:
polarity[sample] = POLARITY
else:
polarity[sample] = polaritySanitizer(row[2])
polarity[sample] = polaritySanitizer(row[polarity_index])
except IOError:
print(f"Error while reading the XCMS tabular file {sample_file}")
raise
Expand Down Expand Up @@ -285,6 +289,9 @@ def xcmsTabular(sample_file, variable_file, matrix_file):
with open(matrix_file, "r") as f:
matrix_data = csv.reader(f, delimiter="\t")
header = next(matrix_data) # list of samples
if header[0] == "":
header[0] = "X"
i = 0
# remove empty columns
# required for W4M-XCMS 1.7
# TODO: check W4M-XCMS 3.0
Expand Down