Merge pull request #745 from davmlaw/issue_744_babelfish_vcf_contig_a…

…ccessions

#744 - babelfish vcf conversion accept contig accessions as chrom names

src/hgvs/extras/babelfish.py

@@ -33,6 +33,8 @@ def __init__(self, hdp, assembly_name):
         )
         self.ac_to_name_map = make_ac_name_map(assembly_name)
         self.name_to_ac_map = make_name_ac_map(assembly_name)
+        # We need to accept accessions as chromosome names, so add them pointing at themselves
+        self.name_to_ac_map.update({ac: ac for ac in self.name_to_ac_map.values()})
 
     def hgvs_to_vcf(self, var_g):
         """**EXPERIMENTAL**

tests/test_hgvs_extras_babelfish.py

@@ -93,3 +93,8 @@ def _v2h(*v):
             hgvs_g = _v2h(*v)
             hgvs_string = hgvs_g.format()
             assert hgvs_string == expected_hgvs_string
+
+
+def test_vcf_to_hgvs_contig_chrom(parser, babelfish38):
+    hgvs_g = babelfish38.vcf_to_g_hgvs("NC_000006.12", 49949409, "GAA", "G")
+    assert hgvs_g.format() == "NC_000006.12:g.49949413_49949414del"