Add additional unittests for outputaccumulator #450
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mschwoer
approved these changes
Jan 27, 2025
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| for frag_start, frag_stop in zip( | ||
| base_precursor_df["frag_start_idx"], base_precursor_df["frag_stop_idx"] | ||
| ): | ||
| frag_corr = fragment_correlation_base_df.iloc[frag_start:frag_stop].values | ||
| frag_intensities = base_fragment_df.iloc[frag_start:frag_stop].values | ||
| # median corr of non zero intensities | ||
| frag_corr = frag_corr[frag_intensities > 0] | ||
| median_frag_corr = np.median(frag_corr) if len(frag_corr) > 0 else 0 | ||
| target_use_for_ms2.append(median_frag_corr > precursor_correlation_cutoff) |
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I feel we are re-building the logic that we want to test here?
An alternative approach would be to use as test data a minimal example DataFrame, with only the relevant columns and only that many rows that the logic can be tested..
Advantages:
- much simpler and readable test
- increased robustness and strictness
cf. e.g. here https://github.com/MannLabs/alphabase/pull/291/files#diff-ee8a98e83ac2eb73798364728cf68e99da2f84c57ce071de56012e639288bd19
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Added some unit test for the ms2 quality post processing step in the output accumulator.
Mainly: