Merge pull request #169 from opentargets/ds_3117_refactor_clumping

Ds 3117 refactor clumping
opentargets · Oct 13, 2023 · cc1f636 · cc1f636
2 parents f8ed420 + 86279b6
commit cc1f636
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Showing 2 changed files with 5 additions and 6 deletions.
diff --git a/src/otg/dataset/summary_statistics.py b/src/otg/dataset/summary_statistics.py
@@ -55,7 +55,6 @@ def window_based_clumping(
         self: SummaryStatistics,
         distance: int,
         gwas_significance: float = 5e-8,
-        with_locus: bool = False,
         baseline_significance: float = 0.05,
         locus_collect_distance: int | None = None,
     ) -> StudyLocus:
@@ -70,10 +69,8 @@ def window_based_clumping(
         Returns:
             StudyLocus: Clumped study-locus containing variants based on window.
         """
-        if locus_collect_distance is None:
-            locus_collect_distance = distance
-        # Based on if we want to get the locus different clumping function is called:
-        if with_locus:
+        # If locus collect distance is present, collect locus with the provided distance:
+        if locus_collect_distance:
             clumped_df = WindowBasedClumping.clump_with_locus(
                 self,
                 window_length=distance,

diff --git a/tests/method/test_window_based_clumping.py b/tests/method/test_window_based_clumping.py
@@ -44,7 +44,9 @@ def test_window_based_clump_with_locus__correctness(
     sample_summary_satistics: SummaryStatistics,
 ) -> None:
     """Test window-based clumping."""
-    clumped = sample_summary_satistics.window_based_clumping(250_000, with_locus=True)
+    clumped = sample_summary_satistics.window_based_clumping(
+        distance=250_000, locus_collect_distance=250_000
+    )
 
     # Asserting the presence of locus key:
     assert "locus" in clumped.df.columns