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GeneFrequencyPipeline.py
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GeneFrequencyPipeline.py
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import glob
import sys
import pandas as pd
geneLocations = {}
geneName = sys.argv[1]
path = r'D:\Projects\Licenta\Exome Analysis Project\saved exomes analysis'
all_files = glob.glob(path + "/*.csv")
# now = round(time.time() * 1000)
print("Gene Frequency Pipeline started")
for file_name in all_files:
try:
truncatedDataFrame = pd.read_csv(file_name, index_col=None, na_values=['NA'],
usecols=["GeneName", "CHROM", "POS"])
filt = truncatedDataFrame['GeneName'] == geneName
filteredDataFrame = truncatedDataFrame[filt]
for index, row in filteredDataFrame.iterrows():
if (row['POS'], row['CHROM']) not in geneLocations:
geneLocations[(row['POS'], row['CHROM'])] = 1
else:
geneLocations[(row['POS'], row['CHROM'])] += 1
except BaseException:
pass
for key, value in geneLocations.items():
print(key[0], key[1], value)
# then = round(time.time() * 1000)
# print(then-now)