Merge branch 'dev' into ds_pairwise_ld

src/gentropy/susie_finemapper.py

@@ -0,0 +1,140 @@
+"""Step to run a finemapping using."""
+
+from __future__ import annotations
+
+from typing import Any
+
+import numpy as np
+import pyspark.sql.functions as f
+from pyspark.sql import DataFrame, Window
+
+from gentropy.common.session import Session
+from gentropy.dataset.study_locus import StudyLocus
+
+
+class SusieFineMapperStep:
+    """SuSie finemaping. It has generic methods to run SuSie fine mapping for a study locus.
+
+    This class/step is the temporary solution of the fine-mapping warpper for the development purposes.
+    In the future this step will be refactored and moved to the methods module.
+    """
+
+    @staticmethod
+    def susie_inf_to_studylocus(
+        susie_output: dict[str, Any],
+        session: Session,
+        _studyId: str,
+        _region: str,
+        variant_index: DataFrame,
+        cs_lbf_thr: float = 2,
+    ) -> StudyLocus:
+        """Convert SuSiE-inf output to studyLocus DataFrame.
+
+        Args:
+            susie_output (dict[str, Any]): SuSiE-inf output dictionary
+            session (Session): Spark session
+            _studyId (str): study ID
+            _region (str): region
+            variant_index (DataFrame): DataFrame with variant information
+            cs_lbf_thr (float): credible set logBF threshold, default is 2
+
+        Returns:
+            StudyLocus: StudyLocus object with fine-mapped credible sets
+        """
+        variants = np.array(
+            [row["variantId"] for row in variant_index.select("variantId").collect()]
+        ).reshape(-1, 1)
+        PIPs = susie_output["PIP"]
+        lbfs = susie_output["lbf_variable"]
+        mu = susie_output["mu"]
+        susie_result = np.hstack((variants, PIPs, lbfs, mu))
+
+        L_snps = PIPs.shape[1]
+
+        # Extracting credible sets
+        order_creds = list(enumerate(susie_output["lbf"]))
+        order_creds.sort(key=lambda x: x[1], reverse=True)
+        cred_sets = None
+        counter = 0
+        for i, cs_lbf_value in order_creds:
+            if counter > 0 and cs_lbf_value < cs_lbf_thr:
+                counter += 1
+                continue
+            counter += 1
+            sorted_arr = susie_result[
+                susie_result[:, i + 1].astype(float).argsort()[::-1]
+            ]
+            cumsum_arr = np.cumsum(sorted_arr[:, i + 1].astype(float))
+            filter_row = np.argmax(cumsum_arr >= 0.99)
+            if filter_row == 0 and cumsum_arr[0] < 0.99:
+                filter_row = len(cumsum_arr)
+            filter_row += 1
+            filtered_arr = sorted_arr[:filter_row]
+            cred_set = filtered_arr[:, [0, i + 1, i + L_snps + 1, i + 2 * L_snps + 1]]
+            win = Window.rowsBetween(
+                Window.unboundedPreceding, Window.unboundedFollowing
+            )
+            cred_set = (
+                session.spark.createDataFrame(
+                    cred_set.tolist(),
+                    ["variantId", "posteriorProbability", "logBF", "beta"],
+                )
+                .join(
+                    variant_index.select(
+                        "variantId",
+                        "chromosome",
+                        "position",
+                    ),
+                    "variantId",
+                )
+                .sort(f.desc("posteriorProbability"))
+                .withColumn(
+                    "locus",
+                    f.collect_list(
+                        f.struct(
+                            f.col("variantId").cast("string").alias("variantId"),
+                            f.col("posteriorProbability")
+                            .cast("double")
+                            .alias("posteriorProbability"),
+                            f.col("logBF").cast("double").alias("logBF"),
+                            f.col("beta").cast("double").alias("beta"),
+                        )
+                    ).over(win),
+                )
+                .limit(1)
+                .withColumns(
+                    {
+                        "studyId": f.lit(_studyId),
+                        "region": f.lit(_region),
+                        "credibleSetIndex": f.lit(counter),
+                        "credibleSetlog10BF": f.lit(cs_lbf_value * 0.4342944819),
+                        "finemappingMethod": f.lit("SuSiE-inf"),
+                    }
+                )
+                .withColumn(
+                    "studyLocusId",
+                    StudyLocus.assign_study_locus_id(
+                        f.col("studyId"), f.col("variantId")
+                    ),
+                )
+                .select(
+                    "studyLocusId",
+                    "studyId",
+                    "region",
+                    "credibleSetIndex",
+                    "locus",
+                    "variantId",
+                    "chromosome",
+                    "position",
+                    "finemappingMethod",
+                    "credibleSetlog10BF",
+                )
+            )
+            if cred_sets is None:
+                cred_sets = cred_set
+            else:
+                cred_sets = cred_sets.unionByName(cred_set)
+        return StudyLocus(
+            _df=cred_sets,
+            _schema=StudyLocus.get_schema(),
+        )

tests/gentropy/method/test_susie_inf.py

@@ -3,7 +3,11 @@
 from __future__ import annotations
 
 import numpy as np
+from gentropy.common.session import Session
+from gentropy.dataset.study_locus import StudyLocus
+from gentropy.dataset.summary_statistics import SummaryStatistics
 from gentropy.method.susie_inf import SUSIE_inf
+from gentropy.susie_finemapper import SusieFineMapperStep
 
 
 class TestSUSIE_inf:
@@ -48,3 +52,28 @@ def test_SUSIE_inf_cred(
         )
         cred = SUSIE_inf.cred_inf(susie_output["PIP"], LD=ld)
         assert cred[0] == [5]
+
+    def test_SUSIE_inf_convert_to_study_locus(
+        self: TestSUSIE_inf,
+        sample_data_for_susie_inf: list[np.ndarray],
+        sample_summary_statistics: SummaryStatistics,
+        session: Session,
+    ) -> None:
+        """Test of SuSiE-inf credible set generator."""
+        ld = sample_data_for_susie_inf[0]
+        z = sample_data_for_susie_inf[1]
+        susie_output = SUSIE_inf.susie_inf(
+            z=z,
+            LD=ld,
+            est_tausq=False,
+        )
+        gwas_df = sample_summary_statistics._df.limit(21)
+        L1 = SusieFineMapperStep.susie_inf_to_studylocus(
+            susie_output=susie_output,
+            session=session,
+            _studyId="sample_id",
+            _region="sample_region",
+            variant_index=gwas_df,
+            cs_lbf_thr=2,
+        )
+        assert isinstance(L1, StudyLocus), "L1 is not an instance of StudyLocus"