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tcezard
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Nov 3, 2025
tcezard
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Nov 5, 2025
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Some quick suggestions but otherwise approved.
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| else: | ||
| logger.warning(f"Unsupported Field: {field}") |
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The ALT in the attribute_mapper.yaml will trigger this warning which is fine for now.
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| seen_sample_names = set() | ||
| uniq_sample_name = [] | ||
| for sample in sample_names: | ||
| if sample not in seen_sample_names: | ||
| seen_sample_names.add(sample) | ||
| uniq_sample_name.append(sample) | ||
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|
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Suggested change
| seen_sample_names = set() | |
| uniq_sample_name = [] | |
| for sample in sample_names: | |
| if sample not in seen_sample_names: | |
| seen_sample_names.add(sample) | |
| uniq_sample_name.append(sample) | |
| uniq_sample_name = list(set(sample_names)) |
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| """This sets up the logger for logging messages""" | ||
| import logging | ||
| import os | ||
| # Create logger for module name | ||
| logger = logging.getLogger(__name__) | ||
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| def set_up_logging(log_path=None): | ||
| # Set up paths | ||
| input_folder = os.path.dirname(__file__) | ||
| output_folder = os.path.join(input_folder, "..","tests", "output") | ||
| if log_path is None: | ||
| log_path = os.path.join(output_folder, "converted.log") | ||
| logging.basicConfig(filename=log_path, | ||
| level=logging.DEBUG, | ||
| format="%(asctime)s - %(levelname)s - %(message)s") | ||
| return log_path No newline at end of file |
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We can keep this for now but we have a whole existing system to manage logging in the pyutils library.
Co-authored-by: Timothee Cezard <tcezard@ebi.ac.uk>
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Format values and headers are present in the VCF file.
Additional refactor to merge multiple files into one attributes file.