patch for KeyError when attempting a direct index lookup for Thermo-s…

[animesh]

…tyle composite spectrum identifiers in mzML files where scan identifiers are formatted strictly as scan=X or integer scan numbers

[Copilot]

🟡 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.

Once you've addressed the issues Copilot identified, you can request another Copilot review.

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 a try/except KeyError and attempts to extract a scan number from spec_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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[levitsky]

Hi,

Thanks for this contribution. I'm having trouble understanding the exact use case. Do you have an example of input for AA_stat that requires this fix? I would appreciate if you could show a snippet of PSM and mzML files, and what software produced them.