adding tx/gx file input type warnings for stringtie#94
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susannasiebert
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Jul 9, 2026
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| line = line.rstrip('\n') | ||
| if line == '' or line.startswith('#'): | ||
| continue | ||
| fields = line.split('\t') | ||
| if fields[0] == 'Gene ID': | ||
| return 'tsv' | ||
| if len(fields) == 9 and 'gene_id "' in fields[8]: | ||
| return 'gtf' | ||
| return None |
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I think this could be greatly simplified by using csv.DictReader. You pass it a file handle and a delimiter and the resulting reader object has a fieldnames list attribute where you can check whether 'Gene ID' in reader.fieldnames or 'gene_id' in reader.fieldnames'.
| def check_stringtie_file_format(args): | ||
| detected_format = sniff_stringtie_format(args.expression_file) | ||
| if args.mode == 'gene' and detected_format == 'gtf': | ||
| logging.warning( |
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Should this be an error instead of a warning? Same question for line 38?
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Closes #78