fix clinvar test
MODIFY
test/test-clinvar.sh
test/test-clinvar.sh
@@ -11,16 +11,15 @@ export -f check
# 1. Test clinvar annotations
####################################################################
echo " clinvar.t01..."
-echo "chr1 985955 0 pathogenic Congenital_myasthenic_syndrome|Myasthenic_syndrome,_congenital,_8 germline MedGen:C0751882,Orphanet:ORPHA590|MedGen:C3808739,OMIM:615120 None
+echo "chr1 985955 1 pathogenic Congenital_myasthenic_syndrome|Myasthenic_syndrome,_congenital,_8 germline MedGen:C0751882,Orphanet:ORPHA590|MedGen:C3808739,OMIM:615120 None
chr1 1199489 0 None None None None None
-chr1 1959699 0 benign/likely_benign,_risk_factor Idiopathic_generalized_epilepsy|Epilepsy,_idiopathic_generalized_10|Epilepsy,_juvenile_myoclonic_7|Generalized_epilepsy_with_febrile_seizures_plus_type_5|not_provided germline Gene:1957,MedGen:C0270850,OMIM:600669,SNOMED_CT:36803009|MedGen:C2751603,OMIM:613060|MedGen:C2751604|MedGen:C3150401|MedGen:CN517202 None
-chr1 161276553 0 pathogenic Roussy-Levy_syndrome|Charcot-Marie-Tooth_disease,_demyelinating,_type_1b|not_provided germline MedGen:C0205713,OMIM:180800,Orphanet:ORPHA3115,SNOMED_CT:45853006|MedGen:C0270912,OMIM:118200,Orphanet:ORPHA101082,SNOMED_CT:42986003|MedGen:CN517202 None
+chr1 1959699 1 benign/likely_benign,_risk_factor Idiopathic_generalized_epilepsy|Epilepsy,_idiopathic_generalized_10|Epilepsy,_juvenile_myoclonic_7|Generalized_epilepsy_with_febrile_seizures_plus_type_5|not_provided germline Gene:1957,MedGen:C0270850,OMIM:600669,SNOMED_CT:36803009|MedGen:C2751603,OMIM:613060|MedGen:C2751604|MedGen:C3150401|MedGen:CN517202 None
+chr1 161276553 1 pathogenic Roussy-Levy_syndrome|Charcot-Marie-Tooth_disease,_demyelinating,_type_1b|not_provided germline MedGen:C0205713,OMIM:180800,Orphanet:ORPHA3115,SNOMED_CT:45853006|MedGen:C0270912,OMIM:118200,Orphanet:ORPHA101082,SNOMED_CT:42986003|MedGen:CN517202 None
chr1 235891431 0 None None None None None
-chr1 247587093 0 not_provided Familial_cold_urticaria unknown MedGen:C0343068,OMIM:120100,Orphanet:ORPHA47045,SNOMED_CT:238687000 None
-chr3 33063141 0 not_provided GM1_gangliosidosis_type_2 somatic MedGen:C0268272,OMIM:230600,Orphanet:ORPHA79256,SNOMED_CT:18756002 None
+chr1 247587093 1 not_provided Familial_cold_urticaria unknown MedGen:C0343068,OMIM:120100,Orphanet:ORPHA47045,SNOMED_CT:238687000 None
+chr3 33063141 1 not_provided GM1_gangliosidosis_type_2 somatic MedGen:C0268272,OMIM:230600,Orphanet:ORPHA79256,SNOMED_CT:18756002 None
chrX 31200832 0 None None None None None
chrX 89963314 0 None None None None None" > exp
-
gemini query -q "select chrom, end, in_omim,
clinvar_sig,
clinvar_disease_name,

fix clinvar test