Merge pull request #3601 from broadinstitute/dev

Dev
broadinstitute · Sep 11, 2023 · 1833316 · 1833316
2 parents 817dbce + 66b0727
commit 1833316
Show file tree

Hide file tree

Showing 2 changed files with 5 additions and 2 deletions.
diff --git a/seqr/utils/search/elasticsearch/constants.py b/seqr/utils/search/elasticsearch/constants.py
@@ -338,7 +338,10 @@ def _get_phenotype_priority_ranks_by_gene(samples, *args):
     'cadd_PHRED': {'response_key': 'cadd'},
     'dbnsfp_DANN_score': {},
     'eigen_Eigen_phred': {},
-    'dbnsfp_VEST4_score': {'response_key': 'vest', 'format_value': lambda x: x and x.split(';')[0]},
+    'dbnsfp_VEST4_score': {
+        'response_key': 'vest',
+        'format_value': lambda x: x and next((v for v in x.split(';') if v != '.'), None),
+    },
     'dbnsfp_MutPred_score': {'response_key': 'mut_pred'},
     'mpc_MPC': {},
     'dbnsfp_MutationTaster_pred': {'response_key': 'mut_taster'},

diff --git a/seqr/utils/search/elasticsearch/es_utils_tests.py b/seqr/utils/search/elasticsearch/es_utils_tests.py
@@ -317,7 +317,7 @@ def call_request_json(self, index=-1):
           'gnomad_genomes_AN': None,
           'dbnsfp_MetaSVM_pred': None,
           'dbnsfp_Polyphen2_HVAR_pred': None,
-          'dbnsfp_VEST4_score': None,
+          'dbnsfp_VEST4_score': '.;.;.;.',
           'clinvar_allele_id': None,
           'gnomad_exomes_Hom': 0,
           'gnomad_exomes_AF_POPMAX_OR_GLOBAL': 0.00016269686320447742,