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fix: repair SusieFinemapperStep to work with new SL schema and fix lo… #957

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merged 5 commits into from
Dec 19, 2024
Merged

fix: repair SusieFinemapperStep to work with new SL schema and fix lo… #957

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04b3081
fix: repair SusieFinemapperStep to work with new SL schema and fix lo…
Daniel-Considine Dec 16, 2024
a582f19
Merge branch 'dev' into dc_susie_fix
Daniel-Considine Dec 17, 2024
4f8afaa
fix: changing schema
Daniel-Considine Dec 18, 2024
1994c67
Merge branch 'dev' into dc_susie_fix
project-defiant Dec 18, 2024
0b639bd
Merge branch 'dev' into dc_susie_fix
Daniel-Considine Dec 19, 2024
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7 changes: 4 additions & 3 deletions src/gentropy/susie_finemapper.py
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Original file line number Diff line number Diff line change
Expand Up @@ -273,7 +273,7 @@ def susie_inf_to_studylocus( # noqa: C901
),
"variantId",
)
.sort(f.desc("posteriorProbability"))
.sort(f.desc(f.col("posteriorProbability").cast("double")))
.withColumn(
"locus",
f.collect_list(
Expand Down Expand Up @@ -896,8 +896,9 @@ def susie_finemapper_one_sl_row_gathered_boundaries( # noqa: C901
logging.warning("Analysis Flags check failed for this study")
return None

schema = StudyLocus.get_schema()
gwas_df = session.spark.createDataFrame([study_locus_row], schema=schema)
gwas_df = session.spark.createDataFrame(
[study_locus_row], StudyLocus.get_schema()
)
exploded_df = gwas_df.select(f.explode("locus").alias("locus"))

result_df = exploded_df.select(
Expand Down
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