test_translate.py

#! /usr/bin/env python3

import unittest

import test_util
import translate

class TestTranslateBaseClass(test_util.TestBaseClass):
    def setUp(self):
        self.genetic_code = {'GUC': 'V', 'ACC': 'T', 'GUA': 'V', 'GUG': 'V', 'ACU': 'T', 'AAC': 'N', 'CCU': 'P', 'UGG': 'W', 'AGC': 'S', 'AUC': 'I', 'CAU': 'H', 'AAU': 'N', 'AGU': 'S', 'GUU': 'V', 'CAC': 'H', 'ACG': 'T', 'CCG': 'P', 'CCA': 'P', 'ACA': 'T', 'CCC': 'P', 'UGU': 'C', 'GGU': 'G', 'UCU': 'S', 'GCG': 'A', 'UGC': 'C', 'CAG': 'Q', 'GAU': 'D', 'UAU': 'Y', 'CGG': 'R', 'UCG': 'S', 'AGG': 'R', 'GGG': 'G', 'UCC': 'S', 'UCA': 'S', 'UAA': '*', 'GGA': 'G', 'UAC': 'Y', 'GAC': 'D', 'UAG': '*', 'AUA': 'I', 'GCA': 'A', 'CUU': 'L', 'GGC': 'G', 'AUG': 'M', 'CUG': 'L', 'GAG': 'E', 'CUC': 'L', 'AGA': 'R', 'CUA': 'L', 'GCC': 'A', 'AAA': 'K', 'AAG': 'K', 'CAA': 'Q', 'UUU': 'F', 'CGU': 'R', 'CGC': 'R', 'CGA': 'R', 'GCU': 'A', 'GAA': 'E', 'AUU': 'I', 'UUG': 'L', 'UUA': 'L', 'UGA': '*', 'UUC': 'F'}

    def run_translate_sequence(self, rna_seq,
            expected_amino_acid_seq,
            gen_code = None):
        if gen_code is None:
            gen_code = self.genetic_code
        key_word_args = {
                "rna_sequence" : rna_seq,
                "genetic_code" : gen_code,
                }
        self.run_test_of_function(
                function = translate.translate_sequence,
                key_word_args = key_word_args,
                expected_result = expected_amino_acid_seq)

    def run_get_all_translations(self, rna_seq,
            expected_result,
            gen_code = None):
        if gen_code is None:
            gen_code = self.genetic_code
        key_word_args = {
                "rna_sequence" : rna_seq,
                "genetic_code" : gen_code,
                }
        result = None
        result_is_exception = False
        try:
            result = translate.get_all_translations(**key_word_args)
        except BaseException as e:
            result_is_exception = True
            result = e
            pass
        if result and (not result_is_exception):
            result = sorted(result)
        if expected_result:
            expected_result = sorted(expected_result)
        self.assertEqual(result, expected_result,
                self.get_failure_message(
                        function = translate.get_all_translations,
                        key_word_args = key_word_args,
                        expected_result = expected_result,
                        result = result,
                        result_is_exception = result_is_exception))

    def run_get_reverse(self, seq, expected_result):
        self.run_test_of_function(
                function = translate.get_reverse,
                key_word_args = {"sequence" : seq},
                expected_result = expected_result)

    def run_get_complement(self, seq, expected_result):
        self.run_test_of_function(
                function = translate.get_complement,
                key_word_args = {"sequence" : seq},
                expected_result = expected_result)

    def run_reverse_and_complement(self, seq, expected_result):
        self.run_test_of_function(
                function = translate.reverse_and_complement,
                key_word_args = {"sequence" : seq},
                expected_result = expected_result)

    def run_get_longest_peptide(self, rna_seq,
            expected_result,
            gen_code = None):
        if gen_code is None:
            gen_code = self.genetic_code
        key_word_args = {
                "rna_sequence" : rna_seq,
                "genetic_code" : gen_code,
                }
        self.run_test_of_function(
                function = translate.get_longest_peptide,
                key_word_args = key_word_args,
                expected_result = expected_result)


class TestTranslateSequence(TestTranslateBaseClass):

    def test_empty_rna_sequence(self):
        rna_seq = ""
        expected_amino_acid_seq = ""
        self.run_translate_sequence(
                rna_seq = rna_seq,
                expected_amino_acid_seq = expected_amino_acid_seq)

    def test_rna_sequence_with_one_base(self):
        rna_seq = "A"
        expected_amino_acid_seq = ""
        self.run_translate_sequence(
                rna_seq = rna_seq,
                expected_amino_acid_seq = expected_amino_acid_seq)

    def test_rna_sequence_with_two_bases(self):
        rna_seq = "AG"
        expected_amino_acid_seq = ""
        self.run_translate_sequence(
                rna_seq = rna_seq,
                expected_amino_acid_seq = expected_amino_acid_seq)

    def test_only_stop_codon(self):
        rna_seq = "UGA"
        expected_amino_acid_seq = ""
        self.run_translate_sequence(
                rna_seq = rna_seq,
                expected_amino_acid_seq = expected_amino_acid_seq)

    def test_one_codon(self):
        rna_seq = "GUC"
        expected_amino_acid_seq = "V"
        self.run_translate_sequence(
                rna_seq = rna_seq,
                expected_amino_acid_seq = expected_amino_acid_seq)

        rna_seq = "GAA"
        expected_amino_acid_seq = "E"
        self.run_translate_sequence(
                rna_seq = rna_seq,
                expected_amino_acid_seq = expected_amino_acid_seq)

    def test_one_codon_lower_case(self):
        rna_seq = "guc"
        expected_amino_acid_seq = "V"
        self.run_translate_sequence(
                rna_seq = rna_seq,
                expected_amino_acid_seq = expected_amino_acid_seq)

        rna_seq = "gaa"
        expected_amino_acid_seq = "E"
        self.run_translate_sequence(
                rna_seq = rna_seq,
                expected_amino_acid_seq = expected_amino_acid_seq)

    def test_no_stop_to_end(self):
        rna_seq = "GUCGAACGA"
        expected_amino_acid_seq = "VER"
        self.run_translate_sequence(
                rna_seq = rna_seq,
                expected_amino_acid_seq = expected_amino_acid_seq)

    def test_no_stop_with_extra_base(self):
        rna_seq = "GUCGAACGAA"
        expected_amino_acid_seq = "VER"
        self.run_translate_sequence(
                rna_seq = rna_seq,
                expected_amino_acid_seq = expected_amino_acid_seq)

    def test_stop_codon_at_end(self):
        rna_seq = "GUCGAACGAUAA"
        expected_amino_acid_seq = "VER"
        self.run_translate_sequence(
                rna_seq = rna_seq,
                expected_amino_acid_seq = expected_amino_acid_seq)

    def test_stop_codon_within(self):
        rna_seq = "GUCGAAUAACGA"
        expected_amino_acid_seq = "VE"
        self.run_translate_sequence(
                rna_seq = rna_seq,
                expected_amino_acid_seq = expected_amino_acid_seq)


class TestGetAllTranslations(TestTranslateBaseClass):

    def test_no_translations(self):
        rna_seq = "GUCGAAUAACGA"
        expected_amino_acid_seqs = []
        self.run_get_all_translations(
                rna_seq = rna_seq,
                expected_result = expected_amino_acid_seqs)

    def test_one_start_at_end(self):
        rna_seq = "GUCGAAUAACGAAUG"
        expected_amino_acid_seqs = ["M"]
        self.run_get_all_translations(
                rna_seq = rna_seq,
                expected_result = expected_amino_acid_seqs)

    def test_two_short_peptides(self):
        rna_seq = "CCUGAAUGACGUACGUAUGACUGCAGUACGUUACGUACG"
        expected_amino_acid_seqs = [
                "MTYV",
                "MTAVRYV",
                ]
        self.run_get_all_translations(
                rna_seq = rna_seq,
                expected_result = expected_amino_acid_seqs)

    def test_two_short_peptides_lower_case(self):
        rna_seq = "ccugaaugacguacguaugacugcaguacguuacguacg"
        expected_amino_acid_seqs = [
                "MTYV",
                "MTAVRYV",
                ]
        self.run_get_all_translations(
                rna_seq = rna_seq,
                expected_result = expected_amino_acid_seqs)

    def test_two_short_peptides_at_beginning(self):
        rna_seq = "AUGACGUACGUAUGACUGCAGUACGUUACGUACG"
        expected_amino_acid_seqs = [
                "MTYV",
                "MTAVRYV",
                ]
        self.run_get_all_translations(
                rna_seq = rna_seq,
                expected_result = expected_amino_acid_seqs)


class TestGetReverse(TestTranslateBaseClass):
    def test_empty_string(self):
        seq = ""
        expected_result = ""
        self.run_get_reverse(seq, expected_result)

    def test_one_base(self):
        seq = "A"
        expected_result = "A"
        self.run_get_reverse(seq, expected_result)

    def test_simple(self):
        seq = "AUGC"
        expected_result = "CGUA"
        self.run_get_reverse(seq, expected_result)

    def test_simple_lower_case(self):
        seq = "augc"
        expected_result = "CGUA"
        self.run_get_reverse(seq, expected_result)


class TestGetComplement(TestTranslateBaseClass):
    def test_empty_string(self):
        seq = ""
        expected_result = ""
        self.run_get_complement(seq, expected_result)

    def test_one_base(self):
        seq = "G"
        expected_result = "C"
        self.run_get_complement(seq, expected_result)

    def test_simple(self):
        seq = "AUGC"
        expected_result = "UACG"
        self.run_get_complement(seq, expected_result)

    def test_simple_lower_case(self):
        seq = "augc"
        expected_result = "UACG"
        self.run_get_complement(seq, expected_result)


class TestReverseAndComplement(TestTranslateBaseClass):
    def test_empty_string(self):
        seq = ""
        expected_result = ""
        self.run_reverse_and_complement(seq, expected_result)

    def test_one_base(self):
        seq = "A"
        expected_result = "U"
        self.run_reverse_and_complement(seq, expected_result)

    def test_simple(self):
        seq = "AUGC"
        expected_result = "GCAU"
        self.run_reverse_and_complement(seq, expected_result)

    def test_simple(self):
        seq = "augc"
        expected_result = "GCAU"
        self.run_reverse_and_complement(seq, expected_result)


class TestGetLongestPeptide(TestTranslateBaseClass):

    def test_no_translations(self):
        rna_seq = "GUCGAAUAACGA"
        # UCGUUAUUCGAC
        expected_amino_acid_seq = ""
        self.run_get_longest_peptide(
                rna_seq = rna_seq,
                expected_result = expected_amino_acid_seq)

    def test_one_start_at_end(self):
        rna_seq = "GUCGAAUAACGAAUG"
        # CAUUCGUUAUUCGAC
        expected_amino_acid_seq = "M"
        self.run_get_longest_peptide(
                rna_seq = rna_seq,
                expected_result = expected_amino_acid_seq)

    def test_two_short_peptides(self):
        rna_seq = "CCUGAAUGACGUACGUAUGACUGCAGUACGUUACGUACG"
        #          CGUACGUAACGUACUGCAGUCAUACGUACGUCAUUCAGG
        expected_amino_acid_seq = "MTAVRYV"
        self.run_get_longest_peptide(
                rna_seq = rna_seq,
                expected_result = expected_amino_acid_seq)

    def test_two_short_peptides_in_rev_comp(self):
        rna_seq = "CGUACGUAACGUACUGCAGUCAUACGUACGUCAUUCAGG"
        #         "CCUGAAUGACGUACGUAUGACUGCAGUACGUUACGUACG"
        expected_amino_acid_seq = "MTAVRYV"
        self.run_get_longest_peptide(
                rna_seq = rna_seq,
                expected_result = expected_amino_acid_seq)

    def test_two_short_peptides_lower_case(self):
        rna_seq = "ccugaaugacguacguaugacugcaguacguuacguacg"
        #          CGUACGUAACGUACUGCAGUCAUACGUACGUCAUUCAGG
        expected_amino_acid_seq = "MTAVRYV"
        self.run_get_longest_peptide(
                rna_seq = rna_seq,
                expected_result = expected_amino_acid_seq)


if __name__ == '__main__':
    unittest.main()