feat: extract-vars writes thinned-out SCV infos (#240) (#258)

Author: holtgrewe

clinvar_data/extract_vars.py

@@ -10,7 +10,10 @@
 import tqdm
 
 from clinvar_data.pbs.clinvar_public import Allele, ClassifiedRecord, VariationArchive
-from clinvar_data.pbs.clinvar_public_pb2 import AggregateClassificationSet
+from clinvar_data.pbs.clinvar_public_pb2 import (
+    AggregateClassificationSet,
+    ClinicalAssertion,
+)
 from clinvar_data.pbs.extracted_vars import (
     ExtractedRcvRecord,
     ExtractedVcvRecord,
@@ -93,6 +96,43 @@ def thin_out_aggregate_classification_set(
         return result
 
 
+def thin_out_clinical_assertions(
+    clinical_assertions: typing.Iterable[ClinicalAssertion],
+) -> list[ClinicalAssertion]:
+    result = []
+    for clinical_assertion in clinical_assertions:
+        entry = ClinicalAssertion()
+        entry.CopyFrom(clinical_assertion)
+        for key in (
+            "clinvar_submission_id",
+            "additional_submitters",
+            "record_status",
+            "attributes",
+            "observed_ins",
+            "simple_allele",
+            "haplotype",
+            "genotype",
+            "trait_set",
+            "citations",
+            "study_name",
+            "study_description",
+            "comments",
+            "submission_names",
+            "date_created",
+            "date_last_updated",
+            "submission_date",
+            "id",
+            "fda_recognized_database",
+        ):
+            entry.ClearField(key)
+        if entry.HasField("clinvar_accession"):
+            entry.clinvar_accession.ClearField("submitter_identifiers")
+        if entry.HasField("classifications"):
+            entry.classifications.ClearField("comments")
+        result.append(entry)
+    return result
+
+
 def run(path_input: str, output_dir: str, gzip_output: bool):
     """Execute the variant extraction."""
     os.makedirs(output_dir, exist_ok=True)
@@ -142,7 +182,6 @@ def run(path_input: str, output_dir: str, gzip_output: bool):
                 for gene in classified_record.simple_allele.genes
                 if gene.HasField("hgnc_id")
             ]
-
             for location in simple_allele.locations or []:
                 for sequence_location in location.sequence_locations or []:
                     record = ExtractedVcvRecord(
@@ -153,6 +192,9 @@ def run(path_input: str, output_dir: str, gzip_output: bool):
                         classifications=(
                             thin_out_aggregate_classification_set(classified_record.classifications)
                         ),
+                        clinical_assertions=(
+                            thin_out_clinical_assertions(classified_record.clinical_assertions)
+                        ),
                         sequence_location=sequence_location,
                         hgnc_ids=hgnc_ids,
                     )

clinvar_data/pbs/class_by_freq_pb2.py

@@ -171,6 +171,7 @@ class ExtractedVcvRecord(google.protobuf.message.Message):
     NAME_FIELD_NUMBER: builtins.int
     VARIATION_TYPE_FIELD_NUMBER: builtins.int
     CLASSIFICATIONS_FIELD_NUMBER: builtins.int
+    CLINICAL_ASSERTIONS_FIELD_NUMBER: builtins.int
     SEQUENCE_LOCATION_FIELD_NUMBER: builtins.int
     HGNC_IDS_FIELD_NUMBER: builtins.int
     name: builtins.str
@@ -193,6 +194,14 @@ class ExtractedVcvRecord(google.protobuf.message.Message):
     def classifications(self) -> clinvar_data.pbs.clinvar_public_pb2.AggregateClassificationSet:
         """Classifications (thinned out)."""
 
+    @property
+    def clinical_assertions(
+        self,
+    ) -> google.protobuf.internal.containers.RepeatedCompositeFieldContainer[
+        clinvar_data.pbs.clinvar_public_pb2.ClinicalAssertion
+    ]:
+        """Clinical assertions (thinned out),"""
+
     @property
     def sequence_location(self) -> clinvar_data.pbs.clinvar_public_pb2.Location.SequenceLocation:
         """The sequence location on one reference."""
@@ -213,6 +222,9 @@ class ExtractedVcvRecord(google.protobuf.message.Message):
         classifications: (
             clinvar_data.pbs.clinvar_public_pb2.AggregateClassificationSet | None
         ) = ...,
+        clinical_assertions: (
+            collections.abc.Iterable[clinvar_data.pbs.clinvar_public_pb2.ClinicalAssertion] | None
+        ) = ...,
         sequence_location: (
             clinvar_data.pbs.clinvar_public_pb2.Location.SequenceLocation | None
         ) = ...,
@@ -236,6 +248,8 @@ class ExtractedVcvRecord(google.protobuf.message.Message):
             b"accession",
             "classifications",
             b"classifications",
+            "clinical_assertions",
+            b"clinical_assertions",
             "hgnc_ids",
             b"hgnc_ids",
             "name",

clinvar_data/pbs/clinvar_public_pb2.py

@@ -68,6 +68,8 @@ message ExtractedVcvRecord {
   VariationType variation_type = 4;
   // Classifications (thinned out).
   clinvar_data.pbs.clinvar_public.AggregateClassificationSet classifications = 5;
+  // Clinical assertions (thinned out),
+  repeated clinvar_data.pbs.clinvar_public.ClinicalAssertion clinical_assertions = 8;
   // The sequence location on one reference.
   clinvar_data.pbs.clinvar_public.Location.SequenceLocation sequence_location = 6;
   // List of HGNC IDs.

clinvar_data/pbs/extracted_vars_pb2.py

@@ -1 +1 @@
-{"accession": {"accession": "VCV000978270", "version": 1}, "rcvs": [{"accession": {"accession": "RCV001256675", "version": 1}, "title": "NM_003937.3(KYNU):c.326G>C (p.Trp109Ser) AND Catel-Manzke syndrome", "classifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "description": {"value": "Pathogenic", "dateLastEvaluated": "2012-01-07T00:00:00Z", "submissionCount": 1}}}}], "name": "NM_003937.3(KYNU):c.326G>C (p.Trp109Ser)", "variationType": "VARIATION_TYPE_SNV", "classifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "description": "Pathogenic", "dateLastEvaluated": "2012-01-07T00:00:00Z", "dateCreated": "2020-09-27T00:00:00Z", "mostRecentSubmission": "2020-09-27T00:00:00Z", "numberOfSubmitters": 1, "numberOfSubmissions": 1}}, "sequenceLocation": {"assembly": "GRCh37", "chr": "CHROMOSOME_2", "accession": "NC_000002.11", "start": 143685263, "stop": 143685263, "displayStart": 143685263, "displayStop": 143685263, "variantLength": 1, "referenceAllele": "G", "alternateAllele": "C", "positionVcf": 143685263, "referenceAlleleVcf": "G", "alternateAlleleVcf": "C"}, "hgncIds": ["HGNC:6469"]}
+{"accession": {"accession": "VCV000978270", "version": 1}, "rcvs": [{"accession": {"accession": "RCV001256675", "version": 1}, "title": "NM_003937.3(KYNU):c.326G>C (p.Trp109Ser) AND Catel-Manzke syndrome", "classifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "description": {"value": "Pathogenic", "dateLastEvaluated": "2012-01-07T00:00:00Z", "submissionCount": 1}}}}], "name": "NM_003937.3(KYNU):c.326G>C (p.Trp109Ser)", "variationType": "VARIATION_TYPE_SNV", "classifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "description": "Pathogenic", "dateLastEvaluated": "2012-01-07T00:00:00Z", "dateCreated": "2020-09-27T00:00:00Z", "mostRecentSubmission": "2020-09-27T00:00:00Z", "numberOfSubmitters": 1, "numberOfSubmissions": 1}}, "sequenceLocation": {"assembly": "GRCh37", "chr": "CHROMOSOME_2", "accession": "NC_000002.11", "start": 143685263, "stop": 143685263, "displayStart": 143685263, "displayStop": 143685263, "variantLength": 1, "referenceAllele": "G", "alternateAllele": "C", "positionVcf": 143685263, "referenceAlleleVcf": "G", "alternateAlleleVcf": "C"}, "hgncIds": ["HGNC:6469"], "clinicalAssertions": [{"clinvarAccession": {"accession": "SCV001433049", "version": 1, "dateUpdated": "2020-09-27T00:00:00Z", "dateCreated": "2020-09-27T00:00:00Z"}, "classifications": {"reviewStatus": "SUBMITTER_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "germlineClassification": "Pathogenic", "dateLastEvaluated": "2012-01-07T00:00:00Z"}, "assertion": "ASSERTION_VARIATION_TO_DISEASE"}]}

clinvar_data/pbs/extracted_vars_pb2.pyi

@@ -1 +1 @@
-{"accession": {"accession": "VCV000978270", "version": 1}, "rcvs": [{"accession": {"accession": "RCV001256675", "version": 1}, "title": "NM_003937.3(KYNU):c.326G>C (p.Trp109Ser) AND Catel-Manzke syndrome", "classifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "description": {"value": "Pathogenic", "dateLastEvaluated": "2012-01-07T00:00:00Z", "submissionCount": 1}}}}], "name": "NM_003937.3(KYNU):c.326G>C (p.Trp109Ser)", "variationType": "VARIATION_TYPE_SNV", "classifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "description": "Pathogenic", "dateLastEvaluated": "2012-01-07T00:00:00Z", "dateCreated": "2020-09-27T00:00:00Z", "mostRecentSubmission": "2020-09-27T00:00:00Z", "numberOfSubmitters": 1, "numberOfSubmissions": 1}}, "sequenceLocation": {"forDisplay": true, "assembly": "GRCh38", "chr": "CHROMOSOME_2", "accession": "NC_000002.12", "start": 142927694, "stop": 142927694, "displayStart": 142927694, "displayStop": 142927694, "variantLength": 1, "positionVcf": 142927694, "referenceAlleleVcf": "G", "alternateAlleleVcf": "C"}, "hgncIds": ["HGNC:6469"]}
+{"accession": {"accession": "VCV000978270", "version": 1}, "rcvs": [{"accession": {"accession": "RCV001256675", "version": 1}, "title": "NM_003937.3(KYNU):c.326G>C (p.Trp109Ser) AND Catel-Manzke syndrome", "classifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "description": {"value": "Pathogenic", "dateLastEvaluated": "2012-01-07T00:00:00Z", "submissionCount": 1}}}}], "name": "NM_003937.3(KYNU):c.326G>C (p.Trp109Ser)", "variationType": "VARIATION_TYPE_SNV", "classifications": {"germlineClassification": {"reviewStatus": "AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "description": "Pathogenic", "dateLastEvaluated": "2012-01-07T00:00:00Z", "dateCreated": "2020-09-27T00:00:00Z", "mostRecentSubmission": "2020-09-27T00:00:00Z", "numberOfSubmitters": 1, "numberOfSubmissions": 1}}, "sequenceLocation": {"forDisplay": true, "assembly": "GRCh38", "chr": "CHROMOSOME_2", "accession": "NC_000002.12", "start": 142927694, "stop": 142927694, "displayStart": 142927694, "displayStop": 142927694, "variantLength": 1, "positionVcf": 142927694, "referenceAlleleVcf": "G", "alternateAlleleVcf": "C"}, "hgncIds": ["HGNC:6469"], "clinicalAssertions": [{"clinvarAccession": {"accession": "SCV001433049", "version": 1, "dateUpdated": "2020-09-27T00:00:00Z", "dateCreated": "2020-09-27T00:00:00Z"}, "classifications": {"reviewStatus": "SUBMITTER_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER", "germlineClassification": "Pathogenic", "dateLastEvaluated": "2012-01-07T00:00:00Z"}, "assertion": "ASSERTION_VARIATION_TO_DISEASE"}]}