# This code is part of the Biopython distribution and governed by its # license. Please see the LICENSE file that should have been included # as part of this package. from __future__ import print_function import array import copy import sys import warnings # Remove unittest2 import after dropping support for Python 2 if sys.version_info[0] < 3: try: import unittest2 as unittest except ImportError: from Bio import MissingPythonDependencyError raise MissingPythonDependencyError("Under Python 2 this test needs the unittest2 library") else: import unittest from Bio import BiopythonWarning from Bio import Alphabet from Bio import Seq from Bio.Alphabet import IUPAC, Gapped from Bio.Data.IUPACData import (ambiguous_dna_complement, ambiguous_rna_complement, ambiguous_dna_values, ambiguous_rna_values) from Bio.Data.CodonTable import TranslationError, standard_dna_table from Bio.Seq import MutableSeq if sys.version_info[0] == 3: array_indicator = "u" else: array_indicator = "c" test_seqs = [ Seq.Seq("TCAAAAGGATGCATCATG", IUPAC.unambiguous_dna), Seq.Seq("T", IUPAC.ambiguous_dna), Seq.Seq("ATGAAACTG"), Seq.Seq("ATGAARCTG"), Seq.Seq("AWGAARCKG"), # Note no U or T Seq.Seq("".join(ambiguous_rna_values)), Seq.Seq("".join(ambiguous_dna_values)), Seq.Seq("".join(ambiguous_rna_values), Alphabet.generic_rna), Seq.Seq("".join(ambiguous_dna_values), Alphabet.generic_dna), Seq.Seq("".join(ambiguous_rna_values), IUPAC.IUPACAmbiguousRNA()), Seq.Seq("".join(ambiguous_dna_values), IUPAC.IUPACAmbiguousDNA()), Seq.Seq("AWGAARCKG", Alphabet.generic_dna), Seq.Seq("AUGAAACUG", Alphabet.generic_rna), Seq.Seq("ATGAAACTG", IUPAC.unambiguous_dna), Seq.Seq("ATGAAA-CTG", Alphabet.Gapped(IUPAC.unambiguous_dna)), Seq.Seq("ATGAAACTGWN", IUPAC.ambiguous_dna), Seq.Seq("AUGAAACUG", Alphabet.generic_rna), Seq.Seq("AUGAAA==CUG", Alphabet.Gapped(Alphabet.generic_rna, "=")), Seq.Seq("AUGAAACUG", IUPAC.unambiguous_rna), Seq.Seq("AUGAAACUGWN", IUPAC.ambiguous_rna), Seq.Seq("ATGAAACTG", Alphabet.generic_nucleotide), Seq.Seq("AUGAAACTG", Alphabet.generic_nucleotide), # U and T Seq.MutableSeq("ATGAAACTG", Alphabet.generic_dna), Seq.MutableSeq("AUGaaaCUG", IUPAC.unambiguous_rna), Seq.Seq("ACTGTCGTCT", Alphabet.generic_protein), ] protein_seqs = [ Seq.Seq("ATCGPK", IUPAC.protein), Seq.Seq("T.CGPK", Alphabet.Gapped(IUPAC.protein, ".")), Seq.Seq("T-CGPK", Alphabet.Gapped(IUPAC.protein, "-")), Seq.Seq("MEDG-KRXR*", Alphabet.Gapped(Alphabet.HasStopCodon(IUPAC.extended_protein, "*"), "-")), Seq.MutableSeq("ME-K-DRXR*XU", Alphabet.Gapped(Alphabet.HasStopCodon( IUPAC.extended_protein, "*"), "-")), Seq.Seq("MEDG-KRXR@", Alphabet.HasStopCodon(Alphabet.Gapped(IUPAC.extended_protein, "-"), "@")), Seq.Seq("ME-KR@", Alphabet.HasStopCodon(Alphabet.Gapped(IUPAC.protein, "-"), "@")), Seq.Seq("MEDG.KRXR@", Alphabet.Gapped(Alphabet.HasStopCodon(IUPAC.extended_protein, "@"), ".")), ] class TestSeq(unittest.TestCase): def setUp(self): self.s = Seq.Seq("TCAAAAGGATGCATCATG", IUPAC.unambiguous_dna) def test_as_string(self): """Test converting Seq to string""" self.assertEqual("TCAAAAGGATGCATCATG", str(self.s)) def test_construction_using_a_seq_object(self): """Test using a Seq object to initialize another Seq object""" with self.assertRaises(TypeError): Seq.Seq(self.s) def test_repr(self): """Test representation of Seq object""" self.assertEqual("Seq('TCAAAAGGATGCATCATG', IUPACUnambiguousDNA())", repr(self.s)) def test_truncated_repr(self): seq = "TCAAAAGGATGCATCATGTCAAAAGGATGCATCATGTCAAAAGGATGCATCATGTCAAAAGGA" expected = "Seq('TCAAAAGGATGCATCATGTCAAAAGGATGCATCATGTCAAAAGGATGC" + \ "ATCATG...GGA', IUPACAmbiguousDNA())" self.assertEqual(expected, repr(Seq.Seq(seq, IUPAC.ambiguous_dna))) def test_length(self): """Test len method on Seq object""" self.assertEqual(18, len(self.s)) def test_first_nucleotide(self): """Test getting first nucleotide of Seq""" self.assertEqual("T", self.s[0]) def test_last_nucleotide(self): """Test getting last nucleotide of Seq""" self.assertEqual("G", self.s[-1]) def test_slicing(self): """Test slicing of Seq""" self.assertEqual("AA", str(self.s[3:5])) def test_reverse(self): """Test reverse using -1 stride""" self.assertEqual("GTACTACGTAGGAAAACT", self.s[::-1]) def test_extract_third_nucleotide(self): """Test extracting every third nucleotide (slicing with stride 3)""" self.assertEqual("TAGTAA", str(self.s[0::3])) self.assertEqual("CAGGTT", str(self.s[1::3])) self.assertEqual("AAACCG", str(self.s[2::3])) def test_alphabet_letters(self): """Test nucleotides in DNA Seq""" self.assertEqual("GATC", self.s.alphabet.letters) def test_alphabet(self): """Test alphabet of derived Seq object""" t = Seq.Seq("T", IUPAC.unambiguous_dna) u = self.s + t self.assertEqual("IUPACUnambiguousDNA()", str(u.alphabet)) def test_length_concatenated_unambiguous_seq(self): """Test length of concatenated Seq object with unambiguous DNA""" t = Seq.Seq("T", IUPAC.unambiguous_dna) u = self.s + t self.assertEqual(19, len(u)) def test_concatenation_of_seq(self): t = Seq.Seq("T", IUPAC.unambiguous_dna) u = self.s + t self.assertEqual(str(self.s) + "T", str(u)) def test_concatenation_error(self): """DNA Seq objects cannot be concatenated with Protein Seq objects.""" with self.assertRaises(TypeError): self.s + Seq.Seq("T", IUPAC.protein) def test_concatenation_of_ambiguous_and_unambiguous_dna(self): """Concatenate Seq object with ambiguous and unambiguous DNA returns ambiguous Seq.""" t = Seq.Seq("T", IUPAC.ambiguous_dna) u = self.s + t self.assertEqual("IUPACAmbiguousDNA()", str(u.alphabet)) def test_ungap(self): self.assertEqual("ATCCCA", str(Seq.Seq("ATC-CCA").ungap("-"))) with self.assertRaises(ValueError): Seq.Seq("ATC-CCA").ungap("--") with self.assertRaises(ValueError): Seq.Seq("ATC-CCA").ungap() class TestSeqStringMethods(unittest.TestCase): def setUp(self): self.s = Seq.Seq("TCAAAAGGATGCATCATG", IUPAC.unambiguous_dna) self.dna = [ Seq.Seq("ATCG", IUPAC.ambiguous_dna), Seq.Seq("gtca", Alphabet.generic_dna), Seq.MutableSeq("GGTCA", Alphabet.generic_dna), Seq.Seq("CTG-CA", Alphabet.Gapped(IUPAC.unambiguous_dna, "-")), ] self.rna = [ Seq.Seq("AUUUCG", IUPAC.ambiguous_rna), Seq.MutableSeq("AUUCG", IUPAC.ambiguous_rna), Seq.Seq("uCAg", Alphabet.generic_rna), Seq.MutableSeq("UC-AG", Alphabet.Gapped(Alphabet.generic_rna, "-")), Seq.Seq("U.CAG", Alphabet.Gapped(Alphabet.generic_rna, ".")), ] self.nuc = [Seq.Seq("ATCG", Alphabet.generic_nucleotide)] self.protein = [ Seq.Seq("ATCGPK", IUPAC.protein), Seq.Seq("atcGPK", Alphabet.generic_protein), Seq.Seq("T.CGPK", Alphabet.Gapped(IUPAC.protein, ".")), Seq.Seq("T-CGPK", Alphabet.Gapped(IUPAC.protein, "-")), Seq.Seq("MEDG-KRXR*", Alphabet.Gapped( Alphabet.HasStopCodon(IUPAC.extended_protein, "*"), "-")), Seq.MutableSeq("ME-K-DRXR*XU", Alphabet.Gapped( Alphabet.HasStopCodon(IUPAC.extended_protein, "*"), "-")), Seq.Seq("MEDG-KRXR@", Alphabet.HasStopCodon( Alphabet.Gapped(IUPAC.extended_protein, "-"), "@")), Seq.Seq("ME-KR@", Alphabet.HasStopCodon(Alphabet.Gapped(IUPAC.protein, "-"), "@")), Seq.Seq("MEDG.KRXR@", Alphabet.Gapped(Alphabet.HasStopCodon( IUPAC.extended_protein, "@"), ".")), ] self.test_chars = ["-", Seq.Seq("-"), Seq.Seq("*"), "-X@"] def test_string_methods(self): for a in self.dna + self.rna + self.nuc + self.protein: if isinstance(a, Seq.Seq): self.assertEqual(str(a.strip()), str(a).strip()) self.assertEqual(str(a.lstrip()), str(a).lstrip()) self.assertEqual(str(a.rstrip()), str(a).rstrip()) self.assertEqual(str(a.lower()), str(a).lower()) self.assertEqual(str(a.upper()), str(a).upper()) def test_hash(self): with warnings.catch_warnings(record=True): hash(self.s) def test_equal_comparison_of_incompatible_alphabets(self): """Test __eq__ comparison method""" with warnings.catch_warnings(record=True): Seq.Seq("TCAAAA", IUPAC.ambiguous_dna) == \ Seq.Seq("TCAAAA", IUPAC.ambiguous_rna) def test_not_equal_comparsion(self): """Test __ne__ comparison method""" self.assertNotEqual(Seq.Seq("TCAAA", IUPAC.ambiguous_dna), Seq.Seq("TCAAAA", IUPAC.ambiguous_dna)) def test_less_than_comparison(self): """Test __lt__ comparison method""" self.assertTrue(self.s[:-1] < self.s) def test_less_than_comparison_of_incompatible_alphabets(self): """Test incompatible alphabet __lt__ comparison method""" seq1 = Seq.Seq("TCAAA", IUPAC.ambiguous_dna) seq2 = Seq.Seq("UCAAAA", IUPAC.ambiguous_rna) with self.assertWarns(BiopythonWarning): self.assertTrue(seq1 < seq2) def test_less_than_comparison_of_incompatible_types(self): """Test incompatible types __lt__ comparison method""" with self.assertRaises(TypeError): self.s < 1 def test_less_than_or_equal_comparison(self): """Test __le__ comparison method""" self.assertTrue(self.s <= self.s) def test_less_than_or_equal_comparison_of_incompatible_alphabets(self): """Test incompatible alphabet __le__ comparison method""" seq1 = Seq.Seq("TCAAA", IUPAC.ambiguous_dna) seq2 = Seq.Seq("UCAAAA", IUPAC.ambiguous_rna) with self.assertWarns(BiopythonWarning): self.assertTrue(seq1 <= seq2) def test_less_than_or_equal_comparison_of_incompatible_types(self): """Test incompatible types __le__ comparison method""" with self.assertRaises(TypeError): self.s <= 1 def test_greater_than_comparison(self): """Test __gt__ comparison method""" self.assertTrue(self.s > self.s[:-1]) def test_greater_than_comparison_of_incompatible_alphabets(self): """Test incompatible alphabet __gt__ comparison method""" seq1 = Seq.Seq("TCAAA", IUPAC.ambiguous_dna) seq2 = Seq.Seq("UCAAAA", IUPAC.ambiguous_rna) with self.assertWarns(BiopythonWarning): self.assertTrue(seq2 > seq1) def test_greater_than_comparison_of_incompatible_types(self): """Test incompatible types __gt__ comparison method""" with self.assertRaises(TypeError): self.s > 1 def test_greater_than_or_equal_comparison(self): """Test __ge__ comparison method""" self.assertTrue(self.s >= self.s) def test_greater_than_or_equal_comparison_of_incompatible_alphabets(self): """Test incompatible alphabet __ge__ comparison method""" seq1 = Seq.Seq("TCAAA", IUPAC.ambiguous_dna) seq2 = Seq.Seq("UCAAAA", IUPAC.ambiguous_rna) with self.assertWarns(BiopythonWarning): self.assertTrue(seq2 >= seq1) def test_greater_than_or_equal_comparison_of_incompatible_types(self): """Test incompatible types __ge__ comparison method""" with self.assertRaises(TypeError): self.s >= 1 def test_add_method_using_wrong_object(self): with self.assertRaises(TypeError): self.s + dict() def test_radd_method(self): self.assertEqual("TCAAAAGGATGCATCATGTCAAAAGGATGCATCATG", str(self.s.__radd__(self.s))) def test_radd_method_using_incompatible_alphabets(self): rna_seq = Seq.Seq("UCAAAA", IUPAC.ambiguous_rna) with self.assertRaises(TypeError): self.s.__radd__(rna_seq) def test_radd_method_using_wrong_object(self): with self.assertRaises(TypeError): self.s.__radd__(dict()) def test_contains_method(self): self.assertIn("AAAA", self.s) def test_startswith(self): self.assertTrue(self.s.startswith("TCA")) self.assertTrue(self.s.startswith(("CAA", "CTA"), 1)) def test_endswith(self): self.assertTrue(self.s.endswith("ATG")) self.assertTrue(self.s.endswith(("ATG", "CTA"))) def test_append_nucleotides(self): self.test_chars.append(Seq.Seq("A", IUPAC.ambiguous_dna)) self.test_chars.append(Seq.Seq("A", IUPAC.ambiguous_rna)) self.test_chars.append(Seq.Seq("A", Alphabet.generic_nucleotide)) self.assertEqual(7, len(self.test_chars)) def test_append_proteins(self): self.test_chars.append(Seq.Seq("K", Alphabet.generic_protein)) self.test_chars.append(Seq.Seq("K-", Alphabet.Gapped( Alphabet.generic_protein, "-"))) self.test_chars.append(Seq.Seq("K@", Alphabet.Gapped(IUPAC.protein, "@"))) self.assertEqual(7, len(self.test_chars)) def test_exception_when_clashing_alphabets(self): """Test by setting up clashing alphabet sequences""" b = Seq.Seq("-", Alphabet.generic_nucleotide) self.assertRaises(TypeError, self.protein[0].strip, b) b = Seq.Seq("-", Alphabet.generic_protein) self.assertRaises(TypeError, self.dna[0].strip, b) def test_stripping_characters(self): for a in self.dna + self.rna + self.nuc + self.protein: for char in self.test_chars: str_char = str(char) if isinstance(a, Seq.Seq): self.assertEqual(str(a.strip(char)), str(a).strip(str_char)) self.assertEqual(str(a.lstrip(char)), str(a).lstrip(str_char)) self.assertEqual(str(a.rstrip(char)), str(a).rstrip(str_char)) def test_finding_characters(self): for a in self.dna + self.rna + self.nuc + self.protein: for char in self.test_chars: str_char = str(char) if isinstance(a, Seq.Seq): self.assertEqual(a.find(char), str(a).find(str_char)) self.assertEqual(a.find(char, 2, -2), str(a).find(str_char, 2, -2)) self.assertEqual(a.rfind(char), str(a).rfind(str_char)) self.assertEqual(a.rfind(char, 2, -2), str(a).rfind(str_char, 2, -2)) def test_counting_characters(self): for a in self.dna + self.rna + self.nuc + self.protein: for char in self.test_chars: str_char = str(char) if isinstance(a, Seq.Seq): self.assertEqual(a.count(char), str(a).count(str_char)) self.assertEqual(a.count(char, 2, -2), str(a).count(str_char, 2, -2)) def test_splits(self): for a in self.dna + self.rna + self.nuc + self.protein: for char in self.test_chars: str_char = str(char) if isinstance(a, Seq.Seq): self.assertEqual([str(x) for x in a.split(char)], str(a).split(str_char)) self.assertEqual([str(x) for x in a.rsplit(char)], str(a).rsplit(str_char)) for max_sep in [0, 1, 2, 999]: self.assertEqual( [str(x) for x in a.split(char, max_sep)], str(a).split(str_char, max_sep)) class TestSeqAddition(unittest.TestCase): def setUp(self): self.dna = [ Seq.Seq("ATCG", IUPAC.ambiguous_dna), Seq.Seq("gtca", Alphabet.generic_dna), Seq.MutableSeq("GGTCA", Alphabet.generic_dna), Seq.Seq("CTG-CA", Alphabet.Gapped(IUPAC.unambiguous_dna, "-")), "TGGTCA", ] self.rna = [ Seq.Seq("AUUUCG", IUPAC.ambiguous_rna), Seq.MutableSeq("AUUCG", IUPAC.ambiguous_rna), Seq.Seq("uCAg", Alphabet.generic_rna), Seq.MutableSeq("UC-AG", Alphabet.Gapped(Alphabet.generic_rna, "-")), Seq.Seq("U.CAG", Alphabet.Gapped(Alphabet.generic_rna, ".")), "UGCAU", ] self.nuc = [ Seq.Seq("ATCG", Alphabet.generic_nucleotide), "UUUTTTACG", ] self.protein = [ Seq.Seq("ATCGPK", IUPAC.protein), Seq.Seq("atcGPK", Alphabet.generic_protein), Seq.Seq("T.CGPK", Alphabet.Gapped(IUPAC.protein, ".")), Seq.Seq("T-CGPK", Alphabet.Gapped(IUPAC.protein, "-")), Seq.Seq("MEDG-KRXR*", Alphabet.Gapped(Alphabet.HasStopCodon( IUPAC.extended_protein, "*"), "-")), Seq.MutableSeq("ME-K-DRXR*XU", Alphabet.Gapped(Alphabet.HasStopCodon( IUPAC.extended_protein, "*"), "-")), "TEDDF", ] def test_addition_dna_rna_with_generic_nucleotides(self): for a in self.dna + self.rna: for b in self.nuc: c = a + b self.assertEqual(str(c), str(a) + str(b)) def test_addition_dna_rna_with_generic_nucleotides_inplace(self): for a in self.dna + self.rna: for b in self.nuc: c = b + a b += a # can't change 'a' as need value next iteration self.assertEqual(c, b) def test_addition_rna_with_rna(self): self.rna.pop(3) for a in self.rna: for b in self.rna: c = a + b self.assertEqual(str(c), str(a) + str(b)) def test_addition_rna_with_rna_inplace(self): self.rna.pop(3) for a in self.rna: for b in self.rna: c = b + a b += a self.assertEqual(c, b) def test_exception_when_added_rna_has_more_than_one_gap_type(self): """Test resulting sequence has gap types '-' and '.'""" with self.assertRaises(ValueError): self.rna[3] + self.rna[4] with self.assertRaises(ValueError): self.rna[3] += self.rna[4] def test_addition_dna_with_dna(self): for a in self.dna: for b in self.dna: c = a + b self.assertEqual(str(c), str(a) + str(b)) def test_addition_dna_with_dna_inplace(self): for a in self.dna: for b in self.dna: c = b + a b += a self.assertEqual(c, b) def test_addition_dna_with_rna(self): self.dna.pop(4) self.rna.pop(5) for a in self.dna: for b in self.rna: with self.assertRaises(TypeError): a + b with self.assertRaises(TypeError): b + a with self.assertRaises(TypeError): a += b with self.assertRaises(TypeError): b += a def test_addition_proteins(self): self.protein.pop(2) for a in self.protein: for b in self.protein: c = a + b self.assertEqual(str(c), str(a) + str(b)) def test_addition_proteins_inplace(self): self.protein.pop(2) for a in self.protein: for b in self.protein: c = b + a b += a self.assertEqual(c, b) def test_exception_when_added_protein_has_more_than_one_gap_type(self): """Test resulting protein has gap types '-' and '.'""" a = Seq.Seq("T.CGPK", Alphabet.Gapped(IUPAC.protein, ".")) b = Seq.Seq("T-CGPK", Alphabet.Gapped(IUPAC.protein, "-")) with self.assertRaises(ValueError): a + b with self.assertRaises(ValueError): a += b def test_exception_when_added_protein_has_several_stop_codon_types(self): """Test resulting protein has stop codon types '*' and '@'""" a = Seq.Seq("MEDG-KRXR@", Alphabet.HasStopCodon( Alphabet.Gapped(IUPAC.extended_protein, "-"), "@")) b = Seq.Seq("MEDG-KRXR*", Alphabet.Gapped( Alphabet.HasStopCodon(IUPAC.extended_protein, "*"), "-")) with self.assertRaises(ValueError): a + b with self.assertRaises(ValueError): a += b def test_exception_when_adding_protein_with_nucleotides(self): for a in self.protein[0:5]: for b in self.dna[0:3] + self.rna[0:4]: with self.assertRaises(TypeError): a + b with self.assertRaises(TypeError): a += b def test_adding_generic_nucleotide_with_other_nucleotides(self): for a in self.nuc: for b in self.dna + self.rna + self.nuc: c = a + b self.assertEqual(str(c), str(a) + str(b)) def test_adding_generic_nucleotide_with_other_nucleotides_inplace(self): for a in self.nuc: for b in self.dna + self.rna + self.nuc: c = b + a b += a self.assertEqual(c, b) class TestSeqMultiplication(unittest.TestCase): def test_mul_method(self): """Test mul method; relies on addition method""" for seq in test_seqs + protein_seqs: self.assertEqual(seq * 3, seq + seq + seq) def test_mul_method_exceptions(self): """Test mul method exceptions""" for seq in test_seqs + protein_seqs: with self.assertRaises(TypeError): seq * 3.0 with self.assertRaises(TypeError): seq * '' def test_rmul_method(self): """Test rmul method; relies on addition method""" for seq in test_seqs + protein_seqs: self.assertEqual(3 * seq, seq + seq + seq) def test_rmul_method_exceptions(self): """Test rmul method exceptions""" for seq in test_seqs + protein_seqs: with self.assertRaises(TypeError): 3.0 * seq with self.assertRaises(TypeError): '' * seq def test_imul_method(self): """Test imul method; relies on addition and mull methods""" for seq in test_seqs + protein_seqs: original_seq = seq * 1 # make a copy seq *= 3 self.assertEqual(seq, original_seq + original_seq + original_seq) def test_imul_method_exceptions(self): """Test imul method exceptions""" for seq in test_seqs + protein_seqs: with self.assertRaises(TypeError): seq *= 3.0 with self.assertRaises(TypeError): seq *= '' class TestMutableSeq(unittest.TestCase): def setUp(self): self.s = Seq.Seq("TCAAAAGGATGCATCATG", IUPAC.unambiguous_dna) self.mutable_s = MutableSeq("TCAAAAGGATGCATCATG", IUPAC.ambiguous_dna) def test_mutableseq_creation(self): """Test creating MutableSeqs in multiple ways""" mutable_s = MutableSeq("TCAAAAGGATGCATCATG", IUPAC.ambiguous_dna) self.assertIsInstance(mutable_s, MutableSeq, "Creating MutableSeq") mutable_s = self.s.tomutable() self.assertIsInstance(mutable_s, MutableSeq, "Converting Seq to mutable") array_seq = MutableSeq(array.array(array_indicator, "TCAAAAGGATGCATCATG"), IUPAC.ambiguous_dna) self.assertIsInstance(array_seq, MutableSeq, "Creating MutableSeq using array") def test_repr(self): self.assertEqual( "MutableSeq('TCAAAAGGATGCATCATG', IUPACAmbiguousDNA())", repr(self.mutable_s)) def test_truncated_repr(self): seq = "TCAAAAGGATGCATCATGTCAAAAGGATGCATCATGTCAAAAGGATGCATCATGTCAAAAGGA" expected = "MutableSeq('TCAAAAGGATGCATCATGTCAAAAGGATGCATCATGTCAAA" + \ "AGGATGCATCATG...GGA', IUPACAmbiguousDNA())" self.assertEqual(expected, repr(MutableSeq(seq, IUPAC.ambiguous_dna))) def test_equal_comparison(self): """Test __eq__ comparison method""" self.assertEqual(self.mutable_s, "TCAAAAGGATGCATCATG") def test_equal_comparison_of_incompatible_alphabets(self): with self.assertWarns(BiopythonWarning): self.mutable_s == MutableSeq('UCAAAAGGA', IUPAC.ambiguous_rna) def test_not_equal_comparison(self): """Test __ne__ comparison method""" self.assertNotEqual(self.mutable_s, "other thing") def test_less_than_comparison(self): """Test __lt__ comparison method""" self.assertTrue(self.mutable_s[:-1] < self.mutable_s) def test_less_than_comparison_of_incompatible_alphabets(self): with self.assertWarns(BiopythonWarning): self.mutable_s[:-1] < MutableSeq("UCAAAAGGAUGCAUCAUG", IUPAC.ambiguous_rna) def test_less_than_comparison_of_incompatible_types(self): with self.assertRaises(TypeError): self.mutable_s < 1 def test_less_than_comparison_without_alphabet(self): self.assertTrue(self.mutable_s[:-1] < "TCAAAAGGATGCATCATG") def test_less_than_or_equal_comparison(self): """Test __le__ comparison method""" self.assertTrue(self.mutable_s[:-1] <= self.mutable_s) def test_less_than_or_equal_comparison_of_incompatible_alphabets(self): with self.assertWarns(BiopythonWarning): self.mutable_s[:-1] <= MutableSeq("UCAAAAGGAUGCAUCAUG", IUPAC.ambiguous_rna) def test_less_than_or_equal_comparison_of_incompatible_types(self): with self.assertRaises(TypeError): self.mutable_s <= 1 def test_less_than_or_equal_comparison_without_alphabet(self): self.assertTrue(self.mutable_s[:-1] <= "TCAAAAGGATGCATCATG") def test_greater_than_comparison(self): """Test __gt__ comparison method""" self.assertTrue(self.mutable_s > self.mutable_s[:-1]) def test_greater_than_comparison_of_incompatible_alphabets(self): with self.assertWarns(BiopythonWarning): self.mutable_s[:-1] > MutableSeq("UCAAAAGGAUGCAUCAUG", IUPAC.ambiguous_rna) def test_greater_than_comparison_of_incompatible_types(self): with self.assertRaises(TypeError): self.mutable_s > 1 def test_greater_than_comparison_without_alphabet(self): self.assertTrue(self.mutable_s > "TCAAAAGGATGCATCAT") def test_greater_than_or_equal_comparison(self): """Test __ge__ comparison method""" self.assertTrue(self.mutable_s >= self.mutable_s) def test_greater_than_or_equal_comparison_of_incompatible_alphabets(self): with self.assertWarns(BiopythonWarning): self.mutable_s[:-1] >= MutableSeq("UCAAAAGGAUGCAUCAUG", IUPAC.ambiguous_rna) def test_greater_than_or_equal_comparison_of_incompatible_types(self): with self.assertRaises(TypeError): self.mutable_s >= 1 def test_greater_than_or_equal_comparison_without_alphabet(self): self.assertTrue(self.mutable_s >= "TCAAAAGGATGCATCATG") def test_add_method(self): """Test adding wrong type to MutableSeq""" with self.assertRaises(TypeError): self.mutable_s + 1234 def test_radd_method(self): self.assertEqual("TCAAAAGGATGCATCATGTCAAAAGGATGCATCATG", self.mutable_s.__radd__(self.mutable_s)) def test_radd_method_incompatible_alphabets(self): with self.assertRaises(TypeError): self.mutable_s.__radd__(MutableSeq("UCAAAAGGA", IUPAC.ambiguous_rna)) def test_radd_method_using_seq_object(self): self.assertEqual("TCAAAAGGATGCATCATGTCAAAAGGATGCATCATG", self.mutable_s.__radd__(self.s)) def test_radd_method_wrong_type(self): with self.assertRaises(TypeError): self.mutable_s.__radd__(1234) def test_as_string(self): self.assertEqual("TCAAAAGGATGCATCATG", str(self.mutable_s)) def test_length(self): self.assertEqual(18, len(self.mutable_s)) def test_converting_to_immutable(self): self.assertIsInstance(self.mutable_s.toseq(), Seq.Seq) def test_first_nucleotide(self): self.assertEqual('T', self.mutable_s[0]) def test_setting_slices(self): self.assertEqual(MutableSeq('CAAA', IUPAC.ambiguous_dna), self.mutable_s[1:5], "Slice mutable seq") self.mutable_s[1:3] = "GAT" self.assertEqual(MutableSeq("TGATAAAGGATGCATCATG", IUPAC.ambiguous_dna), self.mutable_s, "Set slice with string and adding extra nucleotide") self.mutable_s[1:3] = self.mutable_s[5:7] self.assertEqual(MutableSeq("TAATAAAGGATGCATCATG", IUPAC.ambiguous_dna), self.mutable_s, "Set slice with MutableSeq") self.mutable_s[1:3] = array.array(array_indicator, "GAT") self.assertEqual(MutableSeq("TGATTAAAGGATGCATCATG", IUPAC.ambiguous_dna), self.mutable_s, "Set slice with array") def test_setting_item(self): self.mutable_s[3] = "G" self.assertEqual(MutableSeq("TCAGAAGGATGCATCATG", IUPAC.ambiguous_dna), self.mutable_s) def test_deleting_slice(self): del self.mutable_s[4:5] self.assertEqual(MutableSeq("TCAAAGGATGCATCATG", IUPAC.ambiguous_dna), self.mutable_s) def test_deleting_item(self): del self.mutable_s[3] self.assertEqual(MutableSeq("TCAAAGGATGCATCATG", IUPAC.ambiguous_dna), self.mutable_s) def test_appending(self): self.mutable_s.append("C") self.assertEqual(MutableSeq("TCAAAAGGATGCATCATGC", IUPAC.ambiguous_dna), self.mutable_s) def test_inserting(self): self.mutable_s.insert(4, "G") self.assertEqual(MutableSeq("TCAAGAAGGATGCATCATG", IUPAC.ambiguous_dna), self.mutable_s) def test_popping_last_item(self): self.assertEqual("G", self.mutable_s.pop()) def test_remove_items(self): self.mutable_s.remove("G") self.assertEqual(MutableSeq("TCAAAAGATGCATCATG", IUPAC.ambiguous_dna), self.mutable_s, "Remove first G") self.assertRaises(ValueError, self.mutable_s.remove, 'Z') def test_count(self): self.assertEqual(7, self.mutable_s.count("A")) self.assertEqual(2, self.mutable_s.count("AA")) def test_index(self): self.assertEqual(2, self.mutable_s.index("A")) self.assertRaises(ValueError, self.mutable_s.index, "8888") def test_reverse(self): """Test using reverse method""" self.mutable_s.reverse() self.assertEqual(MutableSeq("GTACTACGTAGGAAAACT", IUPAC.ambiguous_dna), self.mutable_s) def test_reverse_with_stride(self): """Test reverse using -1 stride""" self.assertEqual(MutableSeq("GTACTACGTAGGAAAACT", IUPAC.ambiguous_dna), self.mutable_s[::-1]) def test_complement(self): self.mutable_s.complement() self.assertEqual(str("AGTTTTCCTACGTAGTAC"), str(self.mutable_s)) def test_complement_rna(self): seq = Seq.MutableSeq("AUGaaaCUG", IUPAC.unambiguous_rna) seq.complement() self.assertEqual(str("UACuuuGAC"), str(seq)) def test_complement_mixed_aphabets(self): seq = Seq.MutableSeq("AUGaaaCTG") with self.assertRaises(ValueError): seq.complement() def test_complement_rna_string(self): seq = Seq.MutableSeq("AUGaaaCUG") seq.complement() self.assertEqual('UACuuuGAC', str(seq)) def test_complement_dna_string(self): seq = Seq.MutableSeq("ATGaaaCTG") seq.complement() self.assertEqual('TACtttGAC', str(seq)) def test_reverse_complement(self): self.mutable_s.reverse_complement() self.assertEqual("CATGATGCATCCTTTTGA", str(self.mutable_s)) def test_reverse_complement_of_protein(self): seq = Seq.MutableSeq("ACTGTCGTCT", Alphabet.generic_protein) with self.assertRaises(ValueError): seq.reverse_complement() def test_extend_method(self): self.mutable_s.extend("GAT") self.assertEqual(MutableSeq("TCAAAAGGATGCATCATGGAT", IUPAC.ambiguous_dna), self.mutable_s) def test_extend_with_mutable_seq(self): self.mutable_s.extend(MutableSeq("TTT", IUPAC.ambiguous_dna)) self.assertEqual(MutableSeq("TCAAAAGGATGCATCATGTTT", IUPAC.ambiguous_dna), self.mutable_s) def test_delete_stride_slice(self): del self.mutable_s[4:6 - 1] self.assertEqual(MutableSeq("TCAAAGGATGCATCATG", IUPAC.ambiguous_dna), self.mutable_s) def test_extract_third_nucleotide(self): """Test extracting every third nucleotide (slicing with stride 3)""" self.assertEqual(MutableSeq("TAGTAA", IUPAC.ambiguous_dna), self.mutable_s[0::3]) self.assertEqual(MutableSeq("CAGGTT", IUPAC.ambiguous_dna), self.mutable_s[1::3]) self.assertEqual(MutableSeq("AAACCG", IUPAC.ambiguous_dna), self.mutable_s[2::3]) def test_set_wobble_codon_to_n(self): """Test setting wobble codon to N (set slice with stride 3)""" self.mutable_s[2::3] = "N" * len(self.mutable_s[2::3]) self.assertEqual(MutableSeq("TCNAANGGNTGNATNATN", IUPAC.ambiguous_dna), self.mutable_s) class TestUnknownSeq(unittest.TestCase): def setUp(self): self.s = Seq.UnknownSeq(6) def test_construction(self): self.assertEqual("??????", str(Seq.UnknownSeq(6))) self.assertEqual("NNNNNN", str(Seq.UnknownSeq(6, Alphabet.generic_dna))) self.assertEqual("XXXXXX", str(Seq.UnknownSeq(6, Alphabet.generic_protein))) self.assertEqual("??????", str(Seq.UnknownSeq(6, character="?"))) with self.assertRaises(ValueError): Seq.UnknownSeq(-10) with self.assertRaises(ValueError): Seq.UnknownSeq(6, character='??') def test_length(self): self.assertEqual(6, len(self.s)) def test_repr(self): self.assertEqual( "UnknownSeq(6, character='?')", repr(self.s)) def test_add_method(self): seq1 = Seq.UnknownSeq(3, Alphabet.generic_dna) self.assertEqual("??????NNN", str(self.s + seq1)) seq2 = Seq.UnknownSeq(3, Alphabet.generic_dna) self.assertEqual("NNNNNN", str(seq1 + seq2)) def test_getitem_method(self): self.assertEqual("", self.s[-1:-1]) self.assertEqual("?", self.s[1]) self.assertEqual("?", self.s[5:]) self.assertEqual("?", self.s[:1]) self.assertEqual("??", self.s[1:3]) self.assertEqual("???", self.s[1:6:2]) self.assertEqual("????", self.s[1:-1]) with self.assertRaises(ValueError): self.s[1:6:0] def test_count(self): self.assertEqual(6, self.s.count("?")) self.assertEqual(3, self.s.count("??")) self.assertEqual(0, Seq.UnknownSeq(6, character="N").count("?")) self.assertEqual(0, Seq.UnknownSeq(6, character="N").count("??")) self.assertEqual(4, Seq.UnknownSeq(6, character="?").count("?", start=2)) self.assertEqual(2, Seq.UnknownSeq(6, character="?").count("??", start=2)) def test_complement(self): self.s.complement() self.assertEqual(str("??????"), str(self.s)) def test_complement_of_protein(self): """Test reverse complement shouldn't work on a protein!""" seq = Seq.UnknownSeq(6, Alphabet.generic_protein) with self.assertRaises(ValueError): seq.complement() def test_reverse_complement(self): self.s.reverse_complement() self.assertEqual("??????", str(self.s)) def test_reverse_complement_of_protein(self): seq = Seq.UnknownSeq(6, Alphabet.generic_protein) self.assertRaises(ValueError, seq.reverse_complement) def test_transcribe(self): self.assertEqual("??????", self.s.transcribe()) def test_back_transcribe(self): self.assertEqual("??????", self.s.back_transcribe()) def test_upper(self): seq = Seq.UnknownSeq(6, Alphabet.generic_dna) self.assertEqual("NNNNNN", str(seq.upper())) def test_lower(self): seq = Seq.UnknownSeq(6, Alphabet.generic_dna) self.assertEqual("nnnnnn", str(seq.lower())) def test_translation(self): self.assertEqual("XX", str(self.s.translate())) def test_translation_of_proteins(self): seq = Seq.UnknownSeq(6, IUPAC.protein) self.assertRaises(ValueError, seq.translate) def test_ungap(self): seq = Seq.UnknownSeq(7, alphabet=Alphabet.Gapped(Alphabet.DNAAlphabet(), "-")) self.assertEqual("NNNNNNN", str(seq.ungap("-"))) seq = Seq.UnknownSeq(20, alphabet=Alphabet.Gapped(Alphabet.DNAAlphabet(), "-"), character='-') self.assertEqual("", seq.ungap("-")) class TestAmbiguousComplements(unittest.TestCase): def test_ambiguous_values(self): """Test that other tests do not introduce characters to our values""" self.assertFalse("-" in ambiguous_dna_values) self.assertFalse("?" in ambiguous_dna_values) class TestComplement(unittest.TestCase): def test_complement_ambiguous_dna_values(self): for ambig_char, values in sorted(ambiguous_dna_values.items()): compl_values = str( Seq.Seq(values, alphabet=IUPAC.ambiguous_dna).complement()) ambig_values = ( ambiguous_dna_values[ambiguous_dna_complement[ambig_char]]) self.assertEqual(set(compl_values), set(ambig_values)) def test_complement_ambiguous_rna_values(self): for ambig_char, values in sorted(ambiguous_rna_values.items()): compl_values = str( Seq.Seq(values, alphabet=IUPAC.ambiguous_rna).complement()) ambig_values = ( ambiguous_rna_values[ambiguous_rna_complement[ambig_char]]) self.assertEqual(set(compl_values), set(ambig_values)) def test_complement_incompatible_alphabets(self): seq = Seq.Seq("CAGGTU") with self.assertRaises(ValueError): seq.complement() def test_complement_of_mixed_dna_rna(self): seq = "AUGAAACTG" # U and T self.assertRaises(ValueError, Seq.complement, seq) def test_complement_of_rna(self): seq = "AUGAAACUG" self.assertEqual("UACUUUGAC", Seq.complement(seq)) def test_complement_of_dna(self): seq = "ATGAAACTG" self.assertEqual("TACTTTGAC", Seq.complement(seq)) def test_complement_on_proteins(self): """Test complement shouldn't work on a protein!""" for s in protein_seqs: with self.assertRaises(ValueError): Seq.complement(s) with self.assertRaises(ValueError): s.complement() class TestReverseComplement(unittest.TestCase): def test_reverse_complement(self): test_seqs_copy = copy.copy(test_seqs) test_seqs_copy.pop(21) for nucleotide_seq in test_seqs_copy: if not isinstance(nucleotide_seq.alphabet, Alphabet.ProteinAlphabet) and \ isinstance(nucleotide_seq, Seq.Seq): expected = Seq.reverse_complement(nucleotide_seq) self.assertEqual( repr(expected), repr(nucleotide_seq.reverse_complement())) self.assertEqual( repr(expected[::-1]), repr(nucleotide_seq.complement())) self.assertEqual( str(nucleotide_seq.complement()), str(Seq.reverse_complement(nucleotide_seq))[::-1]) self.assertEqual(str(nucleotide_seq.reverse_complement()), str(Seq.reverse_complement(nucleotide_seq))) def test_reverse_complement_of_mixed_dna_rna(self): seq = "AUGAAACTG" # U and T self.assertRaises(ValueError, Seq.reverse_complement, seq) def test_reverse_complement_of_rna(self): seq = "AUGAAACUG" self.assertEqual("CAGUUUCAU", Seq.reverse_complement(seq)) def test_reverse_complement_of_dna(self): seq = "ATGAAACTG" self.assertEqual("CAGTTTCAT", Seq.reverse_complement(seq)) def test_reverse_complement_on_proteins(self): """Test reverse complement shouldn't work on a protein!""" for s in protein_seqs: with self.assertRaises(ValueError): Seq.reverse_complement(s) with self.assertRaises(ValueError): s.reverse_complement() class TestDoubleReverseComplement(unittest.TestCase): def test_reverse_complements(self): """Test double reverse complement preserves the sequence""" sorted_amb_rna = sorted(ambiguous_rna_values) sorted_amb_dna = sorted(ambiguous_dna_values) for sequence in [Seq.Seq("".join(sorted_amb_rna)), Seq.Seq("".join(sorted_amb_dna)), Seq.Seq("".join(sorted_amb_rna), Alphabet.generic_rna), Seq.Seq("".join(sorted_amb_dna), Alphabet.generic_dna), Seq.Seq("".join(sorted_amb_rna).replace("X", ""), IUPAC.IUPACAmbiguousRNA()), Seq.Seq("".join(sorted_amb_dna).replace("X", ""), IUPAC.IUPACAmbiguousDNA()), Seq.Seq("AWGAARCKG")]: # Note no U or T reversed_sequence = sequence.reverse_complement() self.assertEqual(str(sequence), str(reversed_sequence.reverse_complement())) class TestSequenceAlphabets(unittest.TestCase): def test_sequence_alphabets(self): """Sanity test on the test sequence alphabets. See also enhancement bug 2597. """ for nucleotide_seq in test_seqs: if "U" in str(nucleotide_seq).upper(): self.assertNotIsInstance(nucleotide_seq.alphabet, Alphabet.DNAAlphabet) if "T" in str(nucleotide_seq).upper(): self.assertNotIsInstance(nucleotide_seq.alphabet, Alphabet.RNAAlphabet) class TestTranscription(unittest.TestCase): def test_transcription_dna_into_rna(self): for nucleotide_seq in test_seqs: if isinstance(nucleotide_seq.alphabet, Alphabet.DNAAlphabet): expected = Seq.transcribe(nucleotide_seq) self.assertEqual( str(nucleotide_seq).replace("t", "u").replace("T", "U"), str(expected)) def test_transcription_dna_string_into_rna(self): seq = "ATGAAACTG" self.assertEqual("AUGAAACUG", Seq.transcribe(seq)) def test_seq_object_transcription_method(self): for nucleotide_seq in test_seqs: if isinstance(nucleotide_seq.alphabet, Alphabet.DNAAlphabet) and \ isinstance(nucleotide_seq, Seq.Seq): self.assertEqual(repr(Seq.transcribe(nucleotide_seq)), repr(nucleotide_seq.transcribe())) def test_transcription_of_rna(self): """Test transcription shouldn't work on RNA!""" seq = Seq.Seq("AUGAAACUG", IUPAC.ambiguous_rna) with self.assertRaises(ValueError): seq.transcribe() def test_transcription_of_proteins(self): """Test transcription shouldn't work on a protein!""" for s in protein_seqs: with self.assertRaises(ValueError): Seq.transcribe(s) if isinstance(s, Seq.Seq): with self.assertRaises(ValueError): s.transcribe() def test_back_transcribe_rna_into_dna(self): for nucleotide_seq in test_seqs: if isinstance(nucleotide_seq.alphabet, Alphabet.RNAAlphabet): expected = Seq.back_transcribe(nucleotide_seq) self.assertEqual( str(nucleotide_seq).replace("u", "t").replace("U", "T"), str(expected)) def test_back_transcribe_rna_string_into_dna(self): seq = "AUGAAACUG" self.assertEqual("ATGAAACTG", Seq.back_transcribe(seq)) def test_seq_object_back_transcription_method(self): for nucleotide_seq in test_seqs: if isinstance(nucleotide_seq.alphabet, Alphabet.RNAAlphabet) and \ isinstance(nucleotide_seq, Seq.Seq): expected = Seq.back_transcribe(nucleotide_seq) self.assertEqual(repr(nucleotide_seq.back_transcribe()), repr(expected)) def test_back_transcription_of_proteins(self): """Test back-transcription shouldn't work on a protein!""" for s in protein_seqs: with self.assertRaises(ValueError): Seq.back_transcribe(s) if isinstance(s, Seq.Seq): with self.assertRaises(ValueError): s.back_transcribe() def test_back_transcription_of_dna(self): """Test back-transcription shouldn't work on DNA!""" seq = Seq.Seq("ATGAAACTG", IUPAC.ambiguous_dna) with self.assertRaises(ValueError): seq.back_transcribe() class TestTranslating(unittest.TestCase): def setUp(self): self.test_seqs = [ Seq.Seq("TCAAAAGGATGCATCATG", IUPAC.unambiguous_dna), Seq.Seq("ATGAAACTG"), Seq.Seq("ATGAARCTG"), Seq.Seq("AWGAARCKG"), # Note no U or T Seq.Seq("".join(ambiguous_rna_values)), Seq.Seq("".join(ambiguous_dna_values)), Seq.Seq("".join(ambiguous_rna_values), Alphabet.generic_rna), Seq.Seq("".join(ambiguous_dna_values), Alphabet.generic_dna), Seq.Seq("".join(ambiguous_rna_values), IUPAC.IUPACAmbiguousRNA()), Seq.Seq("".join(ambiguous_dna_values), IUPAC.IUPACAmbiguousDNA()), Seq.Seq("AWGAARCKG", Alphabet.generic_dna), Seq.Seq("AUGAAACUG", Alphabet.generic_rna), Seq.Seq("ATGAAACTG", IUPAC.unambiguous_dna), Seq.Seq("ATGAAACTGWN", IUPAC.ambiguous_dna), Seq.Seq("AUGAAACUG", Alphabet.generic_rna), Seq.Seq("AUGAAACUG", IUPAC.unambiguous_rna), Seq.Seq("AUGAAACUGWN", IUPAC.ambiguous_rna), Seq.Seq("ATGAAACTG", Alphabet.generic_nucleotide), Seq.MutableSeq("ATGAAACTG", Alphabet.generic_dna), Seq.MutableSeq("AUGaaaCUG", IUPAC.unambiguous_rna), ] def test_translation(self): for nucleotide_seq in self.test_seqs: nucleotide_seq = nucleotide_seq[:3 * (len(nucleotide_seq) // 3)] if isinstance(nucleotide_seq, Seq.Seq) and \ 'X' not in str(nucleotide_seq): expected = Seq.translate(nucleotide_seq) self.assertEqual(repr(expected), repr(nucleotide_seq.translate())) def test_alphabets_of_translated_seqs(self): def triple_pad(s): """Add N to ensure length is a multiple of three (whole codons).""" while len(s) % 3: s += "N" return s self.assertEqual("IUPACProtein()", repr(self.test_seqs[0].translate().alphabet)) self.assertEqual("ExtendedIUPACProtein()", repr(self.test_seqs[1].translate().alphabet)) self.assertEqual("ExtendedIUPACProtein()", repr(self.test_seqs[2].translate().alphabet)) self.assertEqual("ExtendedIUPACProtein()", repr(self.test_seqs[3].translate().alphabet)) self.assertEqual("ExtendedIUPACProtein()", repr(self.test_seqs[10].translate().alphabet)) self.assertEqual("ExtendedIUPACProtein()", repr(self.test_seqs[11].translate().alphabet)) self.assertEqual("IUPACProtein()", repr(self.test_seqs[12].translate().alphabet)) self.assertEqual( "ExtendedIUPACProtein()", repr(triple_pad(self.test_seqs[13]).translate().alphabet)) self.assertEqual("ExtendedIUPACProtein()", repr(self.test_seqs[14].translate().alphabet)) self.assertEqual("IUPACProtein()", repr(self.test_seqs[15].translate().alphabet)) self.assertEqual( "ExtendedIUPACProtein()", repr(triple_pad(self.test_seqs[16]).translate().alphabet)) self.assertEqual( "ExtendedIUPACProtein()", repr(triple_pad(self.test_seqs[17]).translate().alphabet)) def test_gapped_seq_with_gap_char_given(self): seq = Seq.Seq("ATG---AAACTG") self.assertEqual("M-KL", seq.translate(gap="-")) self.assertRaises(TranslationError, seq.translate, gap="~") def test_gapped_seq_with_stop_codon_and_gap_char_given(self): seq = Seq.Seq("GTG---GCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG") self.assertEqual("V-AIVMGR*KGAR*", seq.translate(gap="-")) self.assertRaises(TranslationError, seq.translate) def test_gapped_seq_with_gap_char_given_and_inferred_from_alphabet(self): seq = Seq.Seq("ATG---AAACTG", Gapped(IUPAC.unambiguous_dna)) self.assertEqual("M-KL", seq.translate(gap="-")) self.assertRaises(ValueError, seq.translate, gap="~") seq = Seq.Seq("ATG~~~AAACTG", Gapped(IUPAC.unambiguous_dna)) self.assertRaises(ValueError, seq.translate, gap="~") self.assertRaises(TranslationError, seq.translate, gap="-") def test_gapped_seq_with_gap_char_given_and_inferred_from_alphabet2(self): """Test using stop codon in sequence""" seq = Seq.Seq("ATG---AAACTGTAG", Gapped(IUPAC.unambiguous_dna)) self.assertEqual("M-KL*", seq.translate(gap="-")) self.assertRaises(ValueError, seq.translate, gap="~") seq = Seq.Seq("ATG---AAACTGTAG", Gapped(IUPAC.unambiguous_dna)) self.assertEqual("M-KL@", seq.translate(gap="-", stop_symbol="@")) self.assertRaises(ValueError, seq.translate, gap="~") seq = Seq.Seq("ATG~~~AAACTGTAG", Gapped(IUPAC.unambiguous_dna)) self.assertRaises(ValueError, seq.translate, gap="~") self.assertRaises(TranslationError, seq.translate, gap="-") def test_gapped_seq_no_gap_char_given(self): seq = Seq.Seq("ATG---AAACTG") self.assertRaises(TranslationError, seq.translate) def test_gapped_seq_no_gap_char_given_and_inferred_from_alphabet(self): seq = Seq.Seq("ATG---AAACTG", Gapped(IUPAC.unambiguous_dna)) self.assertEqual("M-KL", seq.translate()) seq = Seq.Seq("ATG~~~AAACTG", Gapped(IUPAC.unambiguous_dna)) self.assertRaises(TranslationError, seq.translate) seq = Seq.Seq("ATG~~~AAACTG", Gapped(IUPAC.unambiguous_dna, "~")) self.assertEqual("M~KL", seq.translate()) def test_alphabet_of_translated_gapped_seq(self): seq = Seq.Seq("ATG---AAACTG", Gapped(IUPAC.unambiguous_dna)) self.assertEqual("Gapped(ExtendedIUPACProtein(), '-')", repr(seq.translate().alphabet)) seq = Seq.Seq("ATG---AAACTG", Gapped(IUPAC.unambiguous_dna, "-")) self.assertEqual("Gapped(ExtendedIUPACProtein(), '-')", repr(seq.translate().alphabet)) seq = Seq.Seq("ATG~~~AAACTG", Gapped(IUPAC.unambiguous_dna, "~")) self.assertEqual("Gapped(ExtendedIUPACProtein(), '~')", repr(seq.translate().alphabet)) seq = Seq.Seq("ATG---AAACTG") self.assertEqual("Gapped(ExtendedIUPACProtein(), '-')", repr(seq.translate(gap="-").alphabet)) seq = Seq.Seq("ATG~~~AAACTG") self.assertEqual("Gapped(ExtendedIUPACProtein(), '~')", repr(seq.translate(gap="~").alphabet)) seq = Seq.Seq("ATG~~~AAACTGTAG") self.assertEqual( "HasStopCodon(Gapped(ExtendedIUPACProtein(), '~'), '*')", repr(seq.translate(gap="~").alphabet)) seq = Seq.Seq("ATG---AAACTGTGA") self.assertEqual( "HasStopCodon(Gapped(ExtendedIUPACProtein(), '-'), '*')", repr(seq.translate(gap="-").alphabet)) seq = Seq.Seq("ATG---AAACTGTGA") self.assertEqual( "HasStopCodon(Gapped(ExtendedIUPACProtein(), '-'), '@')", repr(seq.translate(gap="-", stop_symbol="@").alphabet)) def test_translation_wrong_type(self): """Test translation table cannot be CodonTable""" seq = Seq.Seq("ATCGTA") with self.assertRaises(ValueError): seq.translate(table=ambiguous_dna_complement) def test_translation_of_string(self): seq = "GTGGCCATTGTAATGGGCCGC" self.assertEqual("VAIVMGR", Seq.translate(seq)) def test_translation_of_gapped_string_with_gap_char_given(self): seq = "GTG---GCCATTGTAATGGGCCGC" expected = "V-AIVMGR" self.assertEqual(expected, Seq.translate(seq, gap="-")) self.assertRaises(TypeError, Seq.translate, seq, gap=[]) self.assertRaises(ValueError, Seq.translate, seq, gap="-*") def test_translation_of_gapped_string_no_gap_char_given(self): seq = "GTG---GCCATTGTAATGGGCCGC" self.assertRaises(TranslationError, Seq.translate, seq) def test_translation_to_stop(self): for nucleotide_seq in self.test_seqs: nucleotide_seq = nucleotide_seq[:3 * (len(nucleotide_seq) // 3)] if isinstance(nucleotide_seq, Seq.Seq) and \ 'X' not in str(nucleotide_seq): short = Seq.translate(nucleotide_seq, to_stop=True) self.assertEqual( str(short), str(Seq.translate(nucleotide_seq).split('*')[0])) seq = "GTGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG" self.assertEqual("VAIVMGRWKGAR", Seq.translate(seq, table=2, to_stop=True)) def test_translation_on_proteins(self): """Test translation shouldn't work on a protein!""" for s in protein_seqs: with self.assertRaises(ValueError): Seq.translate(s) if isinstance(s, Seq.Seq): with self.assertRaises(ValueError): s.translate() def test_translation_of_invalid_codon(self): for codon in ["TA?", "N-N", "AC_", "Ac_"]: with self.assertRaises(TranslationError): Seq.translate(codon) def test_translation_of_glutamine(self): for codon in ['SAR', 'SAG', 'SAA']: self.assertEqual('Z', Seq.translate(codon)) def test_translation_of_asparagine(self): for codon in ['RAY', 'RAT', 'RAC']: self.assertEqual('B', Seq.translate(codon)) def test_translation_of_leucine(self): for codon in ['WTA', 'MTY', 'MTT', 'MTW', 'MTM', 'MTH', 'MTA', 'MTC', 'HTA']: self.assertEqual('J', Seq.translate(codon)) def test_translation_with_bad_table_argument(self): table = dict() with self.assertRaises(ValueError): Seq.translate("GTGGCCATTGTAATGGGCCGC", table=table) def test_translation_with_codon_table_as_table_argument(self): table = standard_dna_table self.assertEqual("VAIVMGR", Seq.translate("GTGGCCATTGTAATGGGCCGC", table=table)) def test_translation_incomplete_codon(self): with self.assertWarns(BiopythonWarning): Seq.translate("GTGGCCATTGTAATGGGCCG") def test_translation_extra_stop_codon(self): seq = "GTGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAGTAG" with self.assertRaises(TranslationError): Seq.translate(seq, table=2, cds=True) def test_translation_using_cds(self): seq = "GTGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG" self.assertEqual("MAIVMGRWKGAR", Seq.translate(seq, table=2, cds=True)) seq = "GTGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCG" # not multiple of three with self.assertRaises(TranslationError): Seq.translate(seq, table=2, cds=True) seq = "GTGGCCATTGTAATGGGCCGCTGAAAGGGTGCCCGA" # no stop codon with self.assertRaises(TranslationError): Seq.translate(seq, table=2, cds=True) seq = "GCCATTGTAATGGGCCGCTGAAAGGGTGCCCGATAG" # no start codon with self.assertRaises(TranslationError): Seq.translate(seq, table=2, cds=True) def test_translation_using_tables_with_ambiguous_stop_codons(self): """Check for error and warning messages. Here, 'ambiguous stop codons' means codons of unambiguous sequence but with a context sensitive encoding as STOP or an amino acid. Thus, these codons appear within the codon table in the forward table as well as in the list of stop codons. """ seq = "ATGGGCTGA" with self.assertRaises(ValueError): Seq.translate(seq, table=28, to_stop=True) with warnings.catch_warnings(record=True) as w: warnings.simplefilter("always") Seq.translate(seq, table=28) message = str(w[-1].message) self.assertTrue(message.startswith("This table contains")) self.assertTrue(message.endswith("be translated as amino acid.")) class TestStopCodons(unittest.TestCase): def setUp(self): self.misc_stops = "TAATAGTGAAGAAGG" def test_stops(self): for nucleotide_seq in [self.misc_stops, Seq.Seq(self.misc_stops), Seq.Seq(self.misc_stops, Alphabet.generic_nucleotide), Seq.Seq(self.misc_stops, Alphabet.DNAAlphabet()), Seq.Seq(self.misc_stops, IUPAC.unambiguous_dna)]: self.assertEqual("***RR", str(Seq.translate(nucleotide_seq))) self.assertEqual("***RR", str(Seq.translate(nucleotide_seq, table=1))) self.assertEqual("***RR", str(Seq.translate(nucleotide_seq, table="SGC0"))) self.assertEqual("**W**", str(Seq.translate(nucleotide_seq, table=2))) self.assertEqual("**WRR", str(Seq.translate(nucleotide_seq, table='Yeast Mitochondrial'))) self.assertEqual("**WSS", str(Seq.translate(nucleotide_seq, table=5))) self.assertEqual("**WSS", str(Seq.translate(nucleotide_seq, table=9))) self.assertEqual("**CRR", str(Seq.translate(nucleotide_seq, table='Euplotid Nuclear'))) self.assertEqual("***RR", str(Seq.translate(nucleotide_seq, table=11))) self.assertEqual("***RR", str(Seq.translate(nucleotide_seq, table='Bacterial'))) def test_translation_of_stops(self): self.assertEqual(Seq.translate("TAT"), "Y") self.assertEqual(Seq.translate("TAR"), "*") self.assertEqual(Seq.translate("TAN"), "X") self.assertEqual(Seq.translate("NNN"), "X") self.assertEqual(Seq.translate("TAt"), "Y") self.assertEqual(Seq.translate("TaR"), "*") self.assertEqual(Seq.translate("TaN"), "X") self.assertEqual(Seq.translate("nnN"), "X") self.assertEqual(Seq.translate("tat"), "Y") self.assertEqual(Seq.translate("tar"), "*") self.assertEqual(Seq.translate("tan"), "X") self.assertEqual(Seq.translate("nnn"), "X") if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)