Merge pull request #109 from cancervariants/error-fixes

Error fixes

Author: korikuzma

setup.py

@@ -1,4 +1,4 @@
 """Module for package and distribution."""
 import setuptools
 
-setuptools.setup(version="0.2.2")
+setuptools.setup(version="0.2.3")

tests/test_normalize.py

@@ -999,7 +999,8 @@ def test_no_matches(test_normalize):
         "ERBB2 G776delinsVCZ", "NP005219.2:p.Glu746_Thr751delinsValAla",
         "NP_005219.2:p.Glu746Thr751delinsValAla", "EGFR L747_L474delinsP",
         "NP_005219.2:p.Glu746_Thr751delinssValAla", "EGFR delins",
-        "NM_004333.4:c.1799_1800delTGinsAT"
+        "NM_004333.4:c.1799_1800delTGinsAT",
+        "NM_173851.3(SLC30A8):c.973C>T%20(p.Arg325Trp)"
     ]
     for q in queries:
         resp = test_normalize.normalize(q)

variant/__init__.py

@@ -6,7 +6,7 @@
 from os import environ
 from gene.query import QueryHandler as GeneQueryHandler
 
-__version__ = "0.2.2"
+__version__ = "0.2.3"
 
 APP_ROOT = Path(__file__).resolve().parents[0]
 

variant/data_sources/transcript_mappings.py

@@ -135,11 +135,11 @@ def protein_transcripts(self, identifier: str,
         if lookup_type == LookupType.GENE_SYMBOL:
             protein_transcripts += \
                 self.ensembl_protein_version_for_gene_symbol.get(
-                    identifier)
+                    identifier, '')
             protein_transcripts += \
-                self.ensembl_protein_for_gene_symbol.get(identifier)
+                self.ensembl_protein_for_gene_symbol.get(identifier, '')
             protein_transcripts += \
-                self.refseq_protein_for_gene_symbol.get(identifier)
+                self.refseq_protein_for_gene_symbol.get(identifier, '')
             return list(set(protein_transcripts))
         else:
             return []
@@ -150,11 +150,12 @@ def coding_dna_transcripts(self, identifier: str,
         genomic_transcripts = list()
         if lookup_type == LookupType.GENE_SYMBOL:
             genomic_transcripts += \
-                self.ensembl_transcript_version_for_gene_symbol.get(identifier)
+                self.ensembl_transcript_version_for_gene_symbol.get(identifier,
+                                                                    '')
             genomic_transcripts += \
-                self.refseq_rna_version_for_gene_symbol.get(identifier)
+                self.refseq_rna_version_for_gene_symbol.get(identifier, '')
             genomic_transcripts += \
-                self.refseq_rna_version_for_gene_symbol.get(identifier)
+                self.refseq_rna_version_for_gene_symbol.get(identifier, '')
             return list(set(genomic_transcripts))
         else:
             return []

variant/validators/genomic_base.py

@@ -53,7 +53,7 @@ def get_nc_accessions_from_nc_accession(self, nc_accession):
                 if a.startswith('GRCh3'):
                     assembly = a
                     break
-        except KeyError:
+        except (KeyError, ValueError):
             pass
         else:
             if assembly: