Merge branch 'dev' into dependabot/pip/ipython-8.30.0

opentargets · Dec 16, 2024 · 62bc314 · 62bc314
2 parents bc47272 + 4820e65
commit 62bc314
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Showing 5 changed files with 20 additions and 317 deletions.
diff --git a/docs/python_api/common/version_engine.md b/docs/python_api/common/version_engine.md
diff --git a/src/gentropy/common/version_engine.py b/src/gentropy/common/version_engine.py
diff --git a/src/gentropy/config.py b/src/gentropy/config.py
@@ -17,7 +17,8 @@ class SessionConfig:
     write_mode: str = "errorifexists"
     spark_uri: str = "local[*]"
     hail_home: str = os.path.dirname(hail_location)
-    extended_spark_conf: dict[str, str] | None = field(default_factory=dict[str, str])
+    extended_spark_conf: dict[str, str] | None = field(
+        default_factory=dict[str, str])
     output_partitions: int = 200
     _target_: str = "gentropy.common.session.Session"
 
@@ -39,7 +40,8 @@ class ColocalisationConfig(StepConfig):
     credible_set_path: str = MISSING
     coloc_path: str = MISSING
     colocalisation_method: str = MISSING
-    colocalisation_method_params: dict[str, Any] = field(default_factory=dict[str, Any])
+    colocalisation_method_params: dict[str, Any] = field(
+        default_factory=dict[str, Any])
     _target_: str = "gentropy.colocalisation.ColocalisationStep"
 
 
@@ -124,7 +126,8 @@ class EqtlCatalogueConfig(StepConfig):
     eqtl_catalogue_paths_imported: str = MISSING
     eqtl_catalogue_study_index_out: str = MISSING
     eqtl_catalogue_credible_sets_out: str = MISSING
-    mqtl_quantification_methods_blacklist: list[str] = field(default_factory=lambda: [])
+    mqtl_quantification_methods_blacklist: list[str] = field(
+        default_factory=lambda: [])
     eqtl_lead_pvalue_threshold: float = 1e-3
     _target_: str = "gentropy.eqtl_catalogue.EqtlCatalogueStep"
 
@@ -146,7 +149,8 @@ class FinngenStudiesConfig(StepConfig):
     )
     finngen_summary_stats_url_suffix: str = ".gz"
     efo_curation_mapping_url: str = "https://raw.githubusercontent.com/opentargets/curation/24.09.1/mappings/disease/manual_string.tsv"
-    sample_size: int = 453733  # https://www.finngen.fi/en/access_results#:~:text=Total%20sample%20size%3A%C2%A0453%2C733%C2%A0(254%2C618%C2%A0females%20and%C2%A0199%2C115%20males)
+    # https://www.finngen.fi/en/access_results#:~:text=Total%20sample%20size%3A%C2%A0453%2C733%C2%A0(254%2C618%C2%A0females%20and%C2%A0199%2C115%20males)
+    sample_size: int = 453733
     _target_: str = "gentropy.finngen_studies.FinnGenStudiesStep"
 
 
@@ -199,7 +203,6 @@ class LDIndexConfig(StepConfig):
             "nfe",  # Non-Finnish European
         ]
     )
-    use_version_from_input: bool = False
     _target_: str = "gentropy.gnomad_ingestion.LDIndexStep"
 
 
@@ -409,7 +412,6 @@ class GnomadVariantConfig(StepConfig):
             "remaining",  # Other
         ]
     )
-    use_version_from_input: bool = False
     _target_: str = "gentropy.gnomad_ingestion.GnomadVariantIndexStep"
 
 
@@ -432,7 +434,6 @@ class PanUKBBConfig(StepConfig):
             "EUR",  # European
         ]
     )
-    use_version_from_input: bool = False
     _target_: str = "gentropy.pan_ukb_ingestion.PanUKBBVariantIndexStep"
 
 
@@ -680,7 +681,8 @@ class Config:
     """Application configuration."""
 
     # this is unfortunately verbose due to @dataclass limitations
-    defaults: List[Any] = field(default_factory=lambda: ["_self_", {"step": MISSING}])
+    defaults: List[Any] = field(default_factory=lambda: [
+                                "_self_", {"step": MISSING}])
     step: StepConfig = MISSING
     datasets: dict[str, str] = field(default_factory=dict)
 
@@ -714,7 +716,8 @@ def register_config() -> None:
         name="gwas_catalog_top_hit_ingestion",
         node=GWASCatalogTopHitIngestionConfig,
     )
-    cs.store(group="step", name="ld_based_clumping", node=LDBasedClumpingConfig)
+    cs.store(group="step", name="ld_based_clumping",
+             node=LDBasedClumpingConfig)
     cs.store(group="step", name="ld_index", node=LDIndexConfig)
     cs.store(group="step", name="locus_to_gene", node=LocusToGeneConfig)
     cs.store(
@@ -732,7 +735,8 @@ def register_config() -> None:
 
     cs.store(group="step", name="pics", node=PICSConfig)
     cs.store(group="step", name="gnomad_variants", node=GnomadVariantConfig)
-    cs.store(group="step", name="ukb_ppp_eur_sumstat_preprocess", node=UkbPppEurConfig)
+    cs.store(group="step", name="ukb_ppp_eur_sumstat_preprocess",
+             node=UkbPppEurConfig)
     cs.store(group="step", name="variant_index", node=VariantIndexConfig)
     cs.store(group="step", name="variant_to_vcf", node=ConvertToVcfStepConfig)
     cs.store(
@@ -765,5 +769,7 @@ def register_config() -> None:
         name="locus_to_gene_associations",
         node=LocusToGeneAssociationsStepConfig,
     )
-    cs.store(group="step", name="finngen_ukb_meta_ingestion", node=FinngenUkbMetaConfig)
-    cs.store(group="step", name="credible_set_qc", node=CredibleSetQCStepConfig)
+    cs.store(group="step", name="finngen_ukb_meta_ingestion",
+             node=FinngenUkbMetaConfig)
+    cs.store(group="step", name="credible_set_qc",
+             node=CredibleSetQCStepConfig)
diff --git a/src/gentropy/gnomad_ingestion.py b/src/gentropy/gnomad_ingestion.py
@@ -4,7 +4,6 @@
 
 from gentropy.common.session import Session
 from gentropy.common.types import LD_Population, VariantPopulation
-from gentropy.common.version_engine import VersionEngine
 from gentropy.config import GnomadVariantConfig, LDIndexConfig
 from gentropy.datasource.gnomad.ld import GnomADLDMatrix
 from gentropy.datasource.gnomad.variants import GnomADVariants
@@ -26,10 +25,10 @@ def __init__(
         min_r2: float = LDIndexConfig().min_r2,
         ld_matrix_template: str = LDIndexConfig().ld_matrix_template,
         ld_index_raw_template: str = LDIndexConfig().ld_index_raw_template,
-        ld_populations: list[LD_Population | str] = LDIndexConfig().ld_populations,
+        ld_populations: list[LD_Population |
+                             str] = LDIndexConfig().ld_populations,
         liftover_ht_path: str = LDIndexConfig().liftover_ht_path,
         grch37_to_grch38_chain_path: str = LDIndexConfig().grch37_to_grch38_chain_path,
-        use_version_from_input: bool = LDIndexConfig().use_version_from_input,
     ) -> None:
         """Run step.
 
@@ -42,17 +41,9 @@ def __init__(
             ld_populations (list[LD_Population | str]): Population names derived from the ld file paths
             liftover_ht_path (str): Path to the liftover ht file
             grch37_to_grch38_chain_path (str): Path to the chain file used to lift over the coordinates.
-            use_version_from_input (bool): Append version derived from input ld_matrix_template to the output ld_index_out. Defaults to False.
 
-        In case use_version_from_input is set to True,
-        data source version inferred from ld_matrix_temolate is appended as the last path segment to the output path.
         Default values are provided in LDIndexConfig.
         """
-        if use_version_from_input:
-            # amend data source version to output path
-            ld_index_out = VersionEngine("gnomad").amend_version(
-                ld_matrix_template, ld_index_out
-            )
         (
             GnomADLDMatrix(
                 ld_matrix_template=ld_matrix_template,
@@ -84,7 +75,6 @@ def __init__(
         gnomad_variant_populations: list[
             VariantPopulation | str
         ] = GnomadVariantConfig().gnomad_variant_populations,
-        use_version_from_input: bool = GnomadVariantConfig().use_version_from_input,
     ) -> None:
         """Run Variant Annotation step.
 
@@ -93,18 +83,10 @@ def __init__(
             variant_annotation_path (str): Path to resulting dataset.
             gnomad_genomes_path (str): Path to gnomAD genomes hail table, e.g. `gs://gcp-public-data--gnomad/release/4.0/ht/genomes/gnomad.genomes.v4.0.sites.ht/`.
             gnomad_variant_populations (list[VariantPopulation | str]): List of populations to include.
-            use_version_from_input (bool): Append version derived from input gnomad_genomes_path to the output variant_annotation_path. Defaults to False.
 
-        In case use_version_from_input is set to True,
-        data source version inferred from gnomad_genomes_path is appended as the last path segment to the output path.
         All defaults are stored in the GnomadVariantConfig.
         """
         # amend data source version to output path
-        if use_version_from_input:
-            variant_annotation_path = VersionEngine("gnomad").amend_version(
-                gnomad_genomes_path, variant_annotation_path
-            )
-
         session.logger.info("Gnomad variant annotation path:")
         session.logger.info(variant_annotation_path)
         # Parse variant info from source.