Merge pull request #55 from biocommons/translation-table-vertebrate-mito

adding vertebrate mitochondrial translate table

src/bioutils/sequences.py

@@ -221,6 +221,16 @@
 dna_to_aa1_sec = dna_to_aa1_lut.copy()
 dna_to_aa1_sec["TGA"] = "U"
 
+# Vertebrate micochondrial translation table
+# https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?chapter=tgencodes#SG2
+
+dna_to_aa1_vmito = dna_to_aa1_lut.copy()
+dna_to_aa1_vmito["AGA"] = "*"
+dna_to_aa1_vmito["AGG"] = "*"
+dna_to_aa1_vmito["ATA"] = "M"
+dna_to_aa1_vmito["TGA"] = "W"
+
+
 complement_transtable = bytes.maketrans(b"ACGT", b"TGCA")
 
 
@@ -506,6 +516,7 @@ class TranslationTable(StrEnum):
 
     standard = "standard"
     selenocysteine = "sec"
+    vertebrate_mitochondrial = "vmito"
 
 
 def translate_cds(seq, full_codons=True, ter_symbol="*", translation_table=TranslationTable.standard):
@@ -596,6 +607,8 @@ def translate_cds(seq, full_codons=True, ter_symbol="*", translation_table=Trans
         trans_table = dna_to_aa1_lut
     elif translation_table == TranslationTable.selenocysteine:
         trans_table = dna_to_aa1_sec
+    elif translation_table == TranslationTable.vertebrate_mitochondrial:
+        trans_table = dna_to_aa1_vmito
     else:
         raise ValueError("Unsupported translation table {}".format(translation_table))
     seq = replace_u_to_t(seq)

tests/test_sequences.py

@@ -42,3 +42,20 @@ def test_translate_selenoproteins():
 
     with pytest.raises(ValueError):
         translate_cds("AUGTGATA", translation_table=TranslationTable.selenocysteine)
+
+
+def test_translate_vertebrate_mitochondrial():
+    """unit test for vertebrate mitochondrial codons"""
+    assert translate_cds("AUGTGATAA") == "M**"
+    assert translate_cds("ATATGAAGGAGA", translation_table=TranslationTable.vertebrate_mitochondrial) == "MW**"
+    assert (
+        translate_cds(
+            "ATAAG",
+            translation_table=TranslationTable.vertebrate_mitochondrial,
+            full_codons=False,
+        )
+        == "M*"
+    )
+
+    with pytest.raises(ValueError):
+        translate_cds("ATAAG", translation_table=TranslationTable.vertebrate_mitochondrial)