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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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62 changes: 60 additions & 2 deletions src/gentropy/susie_finemapper.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,9 @@
from pyspark.sql import DataFrame, Row, Window
from pyspark.sql.functions import desc, row_number
from pyspark.sql.types import (
ArrayType,
DoubleType,
FloatType,
IntegerType,
StringType,
StructField,
Expand Down Expand Up @@ -273,7 +275,7 @@ 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 @@ -896,7 +898,63 @@ 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()
schema = StructType(
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[
StructField("studyLocusId", StringType(), True),
StructField("studyType", StringType(), True),
StructField("variantId", StringType(), True),
StructField("chromosome", StringType(), True),
StructField("position", IntegerType(), True),
StructField("region", StringType(), True),
StructField("studyId", StringType(), True),
StructField("beta", DoubleType(), True),
StructField("zScore", DoubleType(), True),
StructField("pValueMantissa", FloatType(), True),
StructField("pValueExponent", IntegerType(), True),
StructField("effectAlleleFrequencyFromSource", FloatType(), True),
StructField("standardError", DoubleType(), True),
StructField("subStudyDescription", StringType(), True),
StructField("qualityControls", ArrayType(StringType(), True), True),
StructField("finemappingMethod", StringType(), True),
StructField("credibleSetIndex", IntegerType(), True),
StructField("credibleSetlog10BF", DoubleType(), True),
StructField("purityMeanR2", DoubleType(), True),
StructField("purityMinR2", DoubleType(), True),
StructField("locusStart", IntegerType(), True),
StructField("locusEnd", IntegerType(), True),
StructField("sampleSize", IntegerType(), True),
StructField(
"ldSet",
ArrayType(
StructType(
[
StructField("tagVariantId", StringType(), True),
StructField("r2Overall", DoubleType(), True),
]
),
True,
),
True,
),
StructField(
"locus",
ArrayType(
StructType(
[
StructField("variantId", StringType(), True),
StructField("beta", DoubleType(), True),
StructField("pValueMantissa", FloatType(), True),
StructField("pValueExponent", IntegerType(), True),
StructField("standardError", DoubleType(), True),
]
),
False,
),
True,
),
StructField("confidence", StringType(), True),
]
)
gwas_df = session.spark.createDataFrame([study_locus_row], schema=schema)
exploded_df = gwas_df.select(f.explode("locus").alias("locus"))

Expand Down
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