test_hgvs_variantmapper_cp_altseqbuilder.py

# -*- coding: utf-8 -*-
import os
import unittest

import support.mock_input_source as mock_input_data_source

import hgvs.parser
import hgvs.utils.altseqbuilder as altseqbuilder
from hgvs.utils.reftranscriptdata import RefTranscriptData


class TestAltSeqBuilder(unittest.TestCase):
    # root sequence = ""
    fn = os.path.join(os.path.dirname(__file__), "data", "sanity_cp.tsv")
    _datasource = mock_input_data_source.MockInputSource(fn)
    _parser = hgvs.parser.Parser()

    def test_substitution_start(self):
        hgvsc = "NM_999999.1:c.1A>T"
        expected_sequence = "AAAATCAAATTGAAAGCGAAAGCGTTTCGCGCGAAATAGGGG"
        self._run_comparison(hgvsc, expected_sequence)

    def test_substitution_middle(self):
        hgvsc = "NM_999999.1:c.6A>T"
        expected_sequence = "AAAATCAAAATGAATGCGAAAGCGTTTCGCGCGAAATAGGGG"
        self._run_comparison(hgvsc, expected_sequence)

    def test_substitution_end(self):
        hgvsc = "NM_999999.1:c.30G>C"
        expected_sequence = "AAAATCAAAATGAAAGCGAAAGCGTTTCGCGCGAAATACGGG"
        self._run_comparison(hgvsc, expected_sequence)

    # TODO - build in support when system can handle variants in 5'utr region
    # def test_insertion_before_start(self):
    #     hgvsc = "NM_999999.1:c.-1_1insGGG"
    #     expected_sequence = "AAAATCAAAGGGATGAAAGCGAAAGCGTTTCGCGCGAAATAGGGG"
    #     self._run_comparison(hgvsc, expected_sequence)

    def test_insertion_start(self):
        hgvsc = "NM_999999.1:c.1_2insAAA"
        expected_sequence = "AAAATCAAAAAAATGAAAGCGAAAGCGTTTCGCGCGAAATAGGGG"
        self._run_comparison(hgvsc, expected_sequence)

    def test_insertion_middle(self):
        hgvsc = "NM_999999.1:c.22_23insT"
        expected_sequence = "AAAATCAAAATGAAAGCGAAAGCGTTTCGCGTCGAAATAGGGG"
        self._run_comparison(hgvsc, expected_sequence)

    def test_insertion_end(self):
        hgvsc = "NM_999999.1:c.29_30insGG"
        expected_sequence = "AAAATCAAAATGAAAGCGAAAGCGTTTCGCGCGAAATAGGGGGG"
        self._run_comparison(hgvsc, expected_sequence)

    # TODO - build in support when system can handle variants in 3'utr region
    # def test_insertion_after_end(self):
    #     hgvsc = "NM_999999.1:c.30_*1insAA"
    #     expected_sequence = "AAAATCAAAATGAAAGCGAAAGCGTTTCGCGCGAAATAGAAGGGN"
    #     self._run_comparison(hgvsc, expected_sequence)

    def test_deletion_start(self):
        hgvsc = "NM_999999.1:c.1del"
        expected_sequence = "AAAATCAAATGAAAGCGAAAGCGTTTCGCGCGAAATAGGGG"
        self._run_comparison(hgvsc, expected_sequence)

    def test_deletion_middle(self):
        hgvsc = "NM_999999.1:c.2_7del"
        expected_sequence = "AAAATCAAAACGAAAGCGTTTCGCGCGAAATAGGGG"
        self._run_comparison(hgvsc, expected_sequence)

    def test_deletion_end(self):
        hgvsc = "NM_999999.1:c.30del"
        expected_sequence = "AAAATCAAAATGAAAGCGAAAGCGTTTCGCGCGAAATAGGG"
        self._run_comparison(hgvsc, expected_sequence)

    def test_delins_start(self):
        hgvsc = "NM_999999.1:c.1delinsTTTT"
        expected_sequence = "AAAATCAAATTTTTGAAAGCGAAAGCGTTTCGCGCGAAATAGGGG"
        self._run_comparison(hgvsc, expected_sequence)

    def test_delins_middle(self):
        hgvsc = "NM_999999.1:c.2_3delinsAA"
        expected_sequence = "AAAATCAAAAAAAAAGCGAAAGCGTTTCGCGCGAAATAGGGG"
        self._run_comparison(hgvsc, expected_sequence)

    def test_delins_end(self):
        hgvsc = "NM_999999.1:c.30delinsCCCC"
        expected_sequence = "AAAATCAAAATGAAAGCGAAAGCGTTTCGCGCGAAATACCCCGGG"
        self._run_comparison(hgvsc, expected_sequence)

    def test_dup(self):
        hgvsc = "NM_999999.1:c.16_24dup"
        expected_sequence = "AAAATCAAAATGAAAGCGAAAGCGTTTCGCGCGTTTCGCGCGAAATAGGGG"
        self._run_comparison(hgvsc, expected_sequence)

    def test_delete_gene(self):
        hgvsc = "NM_999999.1:c.-3_*1del"
        expected_sequence = ""
        self._run_comparison(hgvsc, expected_sequence)

    def test_sequence_with_length_that_is_not_divisible_by_3(self):
        hgvsc = "NM_999992.2:c.1del"
        with self.assertRaises(NotImplementedError):
            ac_p = "DUMMY"
            var = self._parser.parse_hgvs_variant(hgvsc)
            RefTranscriptData(hdp=self._datasource, tx_ac=var.ac, pro_ac=ac_p)

    # def test_2_substitutions(self):
    #     pass
    #
    # def test_2_indel_no_net_frameshift(self):
    #     pass
    #
    # def test_2_indel_net_frameshift(self):
    #     pass

    def _run_comparison(self, hgvsc, expected_sequence):
        ac_p = "DUMMY"
        var = self._parser.parse_hgvs_variant(hgvsc)
        transcript_data = RefTranscriptData(hdp=self._datasource, tx_ac=var.ac, pro_ac=ac_p)

        builder = altseqbuilder.AltSeqBuilder(var, transcript_data)
        insert_result = builder.build_altseq()
        actual_sequence = insert_result[0].transcript_sequence
        msg = "expected: {}\nactual  : {}".format(expected_sequence, actual_sequence)
        self.assertEqual(expected_sequence, actual_sequence, msg)


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

# <LICENSE>
# Copyright 2018 HGVS Contributors (https://github.com/biocommons/hgvs)
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
# </LICENSE>