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[Python] Read VCF (variant call format) as pandas.DataFrame
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| #!/usr/bin/env python | |
| import io | |
| import os | |
| import pandas as pd | |
| def read_vcf(path): | |
| with open(path, 'r') as f: | |
| lines = [l for l in f if not l.startswith('##')] | |
| return pd.read_csv( | |
| io.StringIO(''.join(lines)), | |
| dtype={'#CHROM': str, 'POS': int, 'ID': str, 'REF': str, 'ALT': str, | |
| 'QUAL': str, 'FILTER': str, 'INFO': str}, | |
| sep='\t' | |
| ).rename(columns={'#CHROM': 'CHROM'}) |
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