Created
July 7, 2024 13:34
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short_read_depth_calculation
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| def depth_calc(file, read_depth=0): | |
| df = pd.read_csv(file, sep='\t', header=None) | |
| df.columns = ['consensus', 'base_position', 'depth'] | |
| plasmid_length = df['base_position'].max() | |
| base_coverage = df[df['depth'] > read_depth].__len__() | |
| cov_perc = (base_coverage/plasmid_length) * 100 | |
| return cov_perc |
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