Fix args.reference_targets AttributeError in U-test fake-test path

[adamklie]

Fix args.reference_targets AttributeError in U-test fake-test path

Summary

Closes #2.

The U-test calibration's compute_fake_perturbation_tests crashes immediately on the first call to compute_perturbation_association because line 160 passes args.reference_targets, which is never defined on the argparse namespace. This makes --compute_fake_perturbation_tests unusable on main.

Change

One-line fix that mirrors the real-test path's fallback logic (lines 44–49). When --guide_annotation_path isn't provided, the real-test path falls back to args.guide_annotation_key (default ['non-targeting']); the fake-test path now does the same.

-                        reference_targets=args.reference_targets,
+                        reference_targets=args.guide_annotation_key,

In the fake-test code path, the relabeled NT subset has guide_targets ∈ {'non-targeting', 'targeting'} (see line 149 where the 6 fake-targeting guides are flipped), so reference_targets=['non-targeting'] is the correct reference set. Using args.guide_annotation_key matches the real-test fallback and respects user override.

Test plan

• Run python U-test_perturbation_calibration.py --compute_fake_perturbation_tests --guide_annotation_path <tsv> --components 30 ... --sel_thresh 2.0 end-to-end on a real dataset (Huangfu HUES8 endoderm differentiation, K=30,50,60,80,100,200,250,300, sel_thresh=2.0).
• Verify per-K <K>_fake_perturbation_association_results.txt files are written in Evaluation/<K>_<sel_thresh>/.
• Verify q-values in the output have a sensible distribution.

Out of scope

Two adjacent issues spotted while debugging — filed/will file separately:

1. main() line 391: pd.concat([test_stats_real_df, test_stats_fake_df], ...) raises NameError when --visualizations is set without --compute_real_perturbation_tests.
2. load_real_perturbation_tests() line 199: hardcoded ['D0', 'D4', 'D7'] sample names. Function is currently unreachable from main() so harmless, but should be parameterized.

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