patch for KeyError when attempting a direct index lookup for Thermo-s… - #14
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animesh wants to merge 1 commit into
Open
patch for KeyError when attempting a direct index lookup for Thermo-s…#14animesh wants to merge 1 commit into
animesh wants to merge 1 commit into
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…tyle composite spectrum identifiers in mzML files where scan identifiers are formatted strictly as scan=X or integer scan numbers
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🟡 Changes recommended
The new fallback still risks KeyError because it only tries the numeric scan as a string, which may not match readers that expect an integer scan number.
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Pull request overview
This PR hardens spectrum lookup in preprocess_spectrum to avoid KeyError when mzML spectrum identifiers are provided in alternate “scan=X” or numeric scan-number formats.
Changes:
- Wraps
reader[spec_id]access in atry/except KeyErrorand attempts to extract a scan number fromspec_id. - Adds fallback lookups using
"scan=<n>"and<n>when the direct lookup fails.
File summaries
| File | Description |
|---|---|
| AA_stat/localization.py | Adds fallback spectrum ID parsing/lookup to handle scan-based IDs and numeric scan numbers. |
Review details
- Files reviewed: 1/1 changed files
- Comments generated: 1
- Review effort level: Lite
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Comment on lines
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| scan_num = match.group(1) | ||
| try: | ||
| original = reader[f"scan={scan_num}"] | ||
| except KeyError: | ||
| original = reader[scan_num] |
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…tyle composite spectrum identifiers in mzML files where scan identifiers are formatted strictly as scan=X or integer scan numbers