Merge remote-tracking branch 'origin/hn-finemapping' into hn-finemapping

src/otg/dataset/fm_data_extraction.py

@@ -172,14 +172,14 @@ def get_matching_snps(
         filtered_LDMatrix = filtered_LDMatrix.filter(filtered_LDMatrix['variantIdCol'].cast('string').isin(unique_variant_ids))
         fm_filtered_LDMatrix = filtered_LDMatrix.drop("variantIdCol")
         return fm_filtered_LDMatrix, fm_filtered_StudyLocus
-    
+
     def allele_flip_check(
         self: FMDataExtraction,
         fm_filtered_StudyLocus: DataFrame,
         SNP_ids_38: list,
     ) -> DataFrame:
         """Check alleles match between LD matrix and summary statistics.
-        
+
             Function unused as currently not needed with gnomad data"""
         df = self.session.createDataFrame(SNP_ids_38, StringType()).toDF("ID")
 

src/otg/method/susie.py

@@ -6,9 +6,9 @@
 
 import numpy as np
 import pandas as pd
-from pyspark.sql import DataFrame
 import scipy.linalg
 import scipy.special
+from pyspark.sql import DataFrame
 from scipy.optimize import minimize, minimize_scalar
 
 from otg.common.session import Session
@@ -17,7 +17,7 @@
 @dataclass
 class SuSiE:
     """SuSiE fine-mapping of a study locus from fine-mapping-inf package.
-    
+
     Copied untested from fine-mapping-inf package as a placeholder
     https://github.com/FinucaneLab/fine-mapping-inf
     """

src/otg/susie.py

@@ -2,7 +2,6 @@
 
 from __future__ import annotations
 
-
 from dataclasses import dataclass
 
 if TYPE_CHECKING:
@@ -14,11 +13,10 @@
 import scipy.linalg
 import scipy.special
 
+from otg.common.session import Session
 from otg.config import SuSiEStepConfig
 from otg.method.susie import SuSiE
 
-from otg.common.session import Session
-
 
 @dataclass
 class SuSiEStep(SuSiEStepConfig):