fixed bugs

[daichengxin]

PR Type

Bug fix

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Description

• Fixed handling of invalid PSMs by properly filtering them out during iteration instead of keeping them in the peptide IDs
• Added tracking of valid peptide hits in a new list to maintain only valid PSMs
• Updated rescore_idxml function to use the filtered peptide IDs list
• Bumped package version from 0.0.2 to 0.0.3

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Changes walkthrough 📝

	Relevant files
Configuration changes	__init__.py Version bump to 0.0.3                                                                        quantmsrescore/init.py Bumped version from 0.0.2 to 0.0.3 +1/-1
Bug fix	ms2rescore.py Fix invalid PSM handling and filtering                                      quantmsrescore/ms2rescore.py Added tracking of valid peptide hits during PSM parsing Fixed handling of invalid PSMs by filtering them out during iteration Updated rescore_idxml to use filtered peptide IDs +9/-2

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PR Reviewer Guide 🔍

Here are some key observations to aid the review process:

⏱️ Estimated effort to review: 2 🔵🔵⚪⚪⚪

🧪 No relevant tests

🔒 No security concerns identified

⚡ Recommended focus areas for review Memory Usage The code creates a new list of peptide IDs which could potentially consume significant memory for large datasets. Consider using a generator pattern or processing in batches. Error Handling The code silently skips invalid PSMs without providing details about why they were invalid. Consider logging more detailed error information. Code Clarity The docstring example shows 'psm_list: return [PSM 1]' which appears to be incomplete or incorrect documentation.

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PR Code Suggestions ✨

Explore these optional code suggestions:

Category	Suggestion	Score
General	Remove or fix invalid type hint that could cause confusion about the variable's purpose The type hint for psm_list appears to be incorrectly formatted as a return value comment. Remove or fix this invalid type hint to avoid confusion. quantmsrescore/ms2rescore.py [63] -psm_list: return [PSM 1] +# psm_list contains PSM objects Apply this suggestion Suggestion importance[1-10]: 7 Why: The line contains an invalid type hint syntax that could cause confusion. Removing or fixing it would improve code clarity and prevent potential misinterpretation.	7

[ypriverol]

This PR is related with the following issue: bigbio/quantms#458