added tests and character validation for ncbi transl_table parser

CountESS-Project · Dec 18, 2019 · 1128e39 · 1128e39
1 parent dadf88d
commit 1128e39
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diff --git a/fqfa/util/translate.py b/fqfa/util/translate.py
@@ -5,6 +5,7 @@
 import itertools
 from typing import Dict, Tuple, Optional
 from fqfa.constants.translation.table import CODON_TABLE
+from fqfa.validator.validator import dna_bases_validator, amino_acids_validator
 
 
 def translate_dna(
@@ -124,6 +125,18 @@ def ncbi_genetic_code_to_dict(ncbi_string: str) -> Dict[str, str]:
     if [len(s) for s in transl_table.values()] != [64] * 5:
         raise ValueError("all transl_table rows must contain 64 characters")
 
+    if not all(
+        dna_bases_validator(bases)
+        for bases in (
+            transl_table["Base1"],
+            transl_table["Base2"],
+            transl_table["Base3"],
+        )
+    ):
+        raise ValueError("transl_table row contains non-DNA base characters")
+    if not amino_acids_validator(transl_table["AAs"]):
+        raise ValueError("transl_table row contains non-amino acid characters")
+
     codon_dict = dict()
     for aa, codon in zip(
         transl_table["AAs"],

diff --git a/tests/test_util_translate.py b/tests/test_util_translate.py
@@ -40,6 +40,115 @@ def test_parsing_default_table(self):
         """
         self.assertDictEqual(ncbi_genetic_code_to_dict(transl_table), CODON_TABLE)
 
+    def test_missing_line(self):
+        transl_table = """
+          AAs  = FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
+          Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+          Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+          Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+        """
+        self.assertRaises(ValueError, ncbi_genetic_code_to_dict, transl_table)
+
+    def test_missing_separator(self):
+        transl_table = """
+          AAs  = FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
+          Starts  ---M------**--*----M---------------M----------------------------
+          Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+          Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+          Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+        """
+        self.assertRaises(ValueError, ncbi_genetic_code_to_dict, transl_table)
+
+        transl_table = """
+          AAs\tFFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
+          Starts\t---M------**--*----M---------------M----------------------------
+          Base1\tTTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+          Base2\tTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+          Base3\tTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+        """
+        self.assertRaises(ValueError, ncbi_genetic_code_to_dict, transl_table)
+
+    def test_wrong_order(self):
+        transl_table = """
+          AAs  = FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
+          Starts = ---M------**--*----M---------------M----------------------------
+          Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+          Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+          Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+        """
+        self.assertRaises(ValueError, ncbi_genetic_code_to_dict, transl_table)
+
+    def test_wrong_length(self):
+        # missing value in one row
+        transl_table = """
+          AAs  = FLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
+          Starts = ---M------**--*----M---------------M----------------------------
+          Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+          Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+          Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+        """
+        self.assertRaises(ValueError, ncbi_genetic_code_to_dict, transl_table)
+
+        # missing value in all rows
+        transl_table = """
+          AAs  = LLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
+          Starts = --M------**--*----M---------------M----------------------------
+          Base1  = TTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+          Base2  = TTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+          Base3  = CAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+        """
+        self.assertRaises(ValueError, ncbi_genetic_code_to_dict, transl_table)
+
+        # extra value in one row
+        transl_table = """
+          AAs  = FFFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
+          Starts = ---M------**--*----M---------------M----------------------------
+          Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+          Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+          Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+        """
+        self.assertRaises(ValueError, ncbi_genetic_code_to_dict, transl_table)
+
+        # extra value in one row
+        transl_table = """
+          AAs  = FFFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
+          Starts = ----M------**--*----M---------------M----------------------------
+          Base1  = TTTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+          Base2  = TTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+          Base3  = TTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+        """
+        self.assertRaises(ValueError, ncbi_genetic_code_to_dict, transl_table)
+
+    def test_nonunique_codons(self):
+        transl_table = """
+          AAs  = FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
+          Starts = ---M------**--*----M---------------M----------------------------
+          Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+          Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+          Base3  = TTAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+        """
+        self.assertRaises(ValueError, ncbi_genetic_code_to_dict, transl_table)
+
+    def test_invalid_bases(self):
+        transl_table = """
+          AAs  = FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
+          Starts = ---M------**--*----M---------------M----------------------------
+          Base1  = WTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+          Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+          Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+        """
+        self.assertRaises(ValueError, ncbi_genetic_code_to_dict, transl_table)
+
+    def test_invalid_aas(self):
+        transl_table = """
+          AAs  = BFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
+          Starts = ---M------**--*----M---------------M----------------------------
+          Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
+          Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
+          Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
+        """
+        self.assertRaises(ValueError, ncbi_genetic_code_to_dict, transl_table)
+
 
 if __name__ == "__main__":
     unittest.main()