Merge branch 'dev' into alegbe-biosample_index

opentargets · Sep 24, 2024 · f93b995 · f93b995
2 parents c9eada2 + 148e26e
commit f93b995
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Showing 3 changed files with 2 additions and 8 deletions.
diff --git a/src/gentropy/dataset/study_index.py b/src/gentropy/dataset/study_index.py
@@ -32,15 +32,13 @@ class StudyQualityCheck(Enum):
         UNKNOWN_STUDY_TYPE (str): Indicating the provided type of study is not supported.
         UNKNOWN_BIOSAMPLE (str): Flagging if a biosample identifier is not found in the reference.
         DUPLICATED_STUDY (str): Flagging if a study identifier is not unique.
-        NO_GENE_PROVIDED (str): Flagging QTL studies if the measured
     """
 
     UNRESOLVED_TARGET = "Target/gene identifier could not match to reference."
     UNRESOLVED_DISEASE = "No valid disease identifier found."
     UNKNOWN_STUDY_TYPE = "This type of study is not supported."
     UNKNOWN_BIOSAMPLE = "Biosample identifier was not found in the reference."
     DUPLICATED_STUDY = "The identifier of this study is not unique."
-    NO_GENE_PROVIDED = "QTL study doesn't have gene assigned."
 
 
 @dataclass

diff --git a/src/gentropy/study_locus_validation.py b/src/gentropy/study_locus_validation.py
@@ -41,14 +41,11 @@ def __init__(
         # Running validation then writing output:
         study_locus_with_qc = (
             StudyLocus.from_parquet(session, list(study_locus_path))
-            # Flagging study locus with subsignificant p-values
-            .validate_lead_pvalue(pvalue_cutoff=gwas_significance)
             # Add flag for MHC region
             .qc_MHC_region()
             .validate_study(study_index)  # Flagging studies not in study index
-            .annotate_study_type(study_index) # Add study type to study locus
+            .annotate_study_type(study_index)  # Add study type to study locus
             .qc_redundant_top_hits_from_PICS()  # Flagging top hits from studies with PICS summary statistics
-            .validate_unique_study_locus_id()  # Flagging duplicated study locus ids
         ).persist()  # we will need this for 2 types of outputs
 
         study_locus_with_qc.valid_rows(

diff --git a/src/gentropy/study_validation.py b/src/gentropy/study_validation.py
@@ -62,8 +62,7 @@ def __init__(
 
         # Running validation:
         study_index_with_qc = (
-            study_index.validate_disease(disease_index)
-            .validate_unique_study_id()  # Flagging duplicated study ids
+            study_index.validate_unique_study_id()  # Flagging duplicated study ids
             .validate_study_type()  # Flagging non-supported study types.
             .validate_target(target_index)  # Flagging QTL studies with invalid targets
             .validate_disease(disease_index)  # Flagging invalid EFOs