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November 3, 2025 21:57
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Extract Quantification Windows from CRISPResso Runs
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| """Report the quantification window indexes used from a CRISPResso run. | |
| The script expects to be adjacent to any number of CRISPResso runs, it will | |
| search among the runs and extract each CRISPResso2_info.json file and print | |
| out the quantification windows for each amplicon. | |
| """ | |
| import glob | |
| import json | |
| def print_qwc(c2_info_path): | |
| with open(c2_info_path) as fh: | |
| c2_info = json.load(fh) | |
| for amplicon in c2_info['results']['ref_names']: | |
| if isinstance(c2_info['results']['refs'][amplicon]['include_idxs'], dict): | |
| print(f'{c2_info_path} QWC for {amplicon}', c2_info['results']['refs'][amplicon]['include_idxs']['value']) | |
| else: | |
| print(f'{c2_info_path} QWC for {amplicon}', c2_info['results']['refs'][amplicon]['include_idxs']) | |
| if __name__ == '__main__': | |
| for c2_info_path in glob.glob(f'./*/**/CRISPResso2_info.json'): | |
| print_qwc(c2_info_path) |
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