25 lines
882 B
Python
25 lines
882 B
Python
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#!/usr/bin/python
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"""
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组织双样本过滤
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"""
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import pandas as pd
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def main(path):
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muts = pd.read_csv(path, sep='\t')
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muts['freq'] = muts['Otherinfo11'].str.extract(r'AF=([\d.]+)')
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# muts['total_reads'] = muts['Otherinfo11'].str.extract(r'DP=(\d+)')
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# muts['mutant_reads'] = muts['Otherinfo11'].str.extract(r'VD=(\d+)')
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muts['Tag'] = 'pass'
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muts.loc[muts['ExonicFunc.refGene'] == 'synonymous SNV', 'Tag'] = 'synonymous'
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muts.loc[muts['ExonicFunc.refGene'] == 'unknown', 'Tag'] = 'unknown_snp'
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tmdf1 = muts[
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['1000g2015aug_all', '1000g2015aug_eas', 'esp6500siv2_all', 'ExAC_nontcga_ALL', 'ExAC_nontcga_EAS',
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'gnomAD_genome_ALL', 'gnomAD_genome_EAS']].replace('.', 0).applymap(lambda x: eval(str(x)))
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muts['freq_high'] = tmdf1.max(axis=1)
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muts.loc[muts['freq_high'] > 0.01, 'Tag'] = 'common_snp'
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