annotate clipkit_repo/tests/unit/test_modes.py @ 0:49b058e85902 draft

"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"

import pytest
from pathlib import Path

import numpy as np
from Bio import AlignIO
from clipkit.modes import TrimmingMode, trim, shouldKeep

here = Path(__file__)


class TestModes(object):
    def test_shouldKeep_kpi_gappy_keep(self):
        ## setup
        mode = TrimmingMode.kpi_gappy
        gappyness = 0.00
        gaps = 0.9
        parsimony_informative = True
        constant_site = False

        assert True == shouldKeep(
            mode, parsimony_informative, constant_site, gappyness, gaps
        )

    def test_shouldKeep_kpi_gappy_trim(self):
        ## setup
        mode = TrimmingMode.kpi_gappy
        gappyness = 0.00
        gaps = 0.9
        parsimony_informative = False
        constant_site = False

        assert False == shouldKeep(
            mode, parsimony_informative, constant_site, gappyness, gaps
        )

    def test_shouldKeep_gappy_keep(self):
        ## setup
        mode = TrimmingMode.gappy
        gappyness = 0.00
        gaps = 0.9
        parsimony_informative = True
        constant_site = False

        assert True == shouldKeep(
            mode, parsimony_informative, constant_site, gappyness, gaps
        )

    def test_shouldKeep_gappy_trim(self):
        ## setup
        mode = TrimmingMode.gappy
        gappyness = 0.95
        gaps = 0.9
        parsimony_informative = True
        constant_site = False

        assert False == shouldKeep(
            mode, parsimony_informative, constant_site, gappyness, gaps
        )

    def test_shouldKeep_kpi_keep(self):
        ## setup
        mode = TrimmingMode.kpi
        gappyness = 0.00
        gaps = 0.9
        parsimony_informative = True
        constant_site = False

        assert True == shouldKeep(
            mode, parsimony_informative, constant_site, gappyness, gaps
        )

    def test_shouldKeep_kpi_trim(self):
        ## setup
        mode = TrimmingMode.kpi
        gappyness = 0.95
        gaps = 0.9
        parsimony_informative = False
        constant_site = False

        assert False == shouldKeep(
            mode, parsimony_informative, constant_site, gappyness, gaps
        )

    def test_shouldKeep_kpic_keep(self):
        ## setup
        mode = TrimmingMode.kpic
        gappyness = 0.95
        gaps = 0.9
        parsimony_informative = False
        constant_site = True

        assert True == shouldKeep(
            mode, parsimony_informative, constant_site, gappyness, gaps
        )

    def test_shouldKeep_kpic_trim(self):
        ## setup
        mode = TrimmingMode.kpic
        gappyness = 0.95
        gaps = 0.9
        parsimony_informative = False
        constant_site = False

        assert False == shouldKeep(
            mode, parsimony_informative, constant_site, gappyness, gaps
        )

    def test_shouldKeep_kpic_gappy_keep(self):
        ## setup
        mode = TrimmingMode.kpic_gappy
        gappyness = 0.70
        gaps = 0.9
        parsimony_informative = False
        constant_site = True

        assert True == shouldKeep(
            mode, parsimony_informative, constant_site, gappyness, gaps
        )

    def test_shouldKeep_kpic_gappy_trim(self):
        ## setup
        mode = TrimmingMode.kpic_gappy
        gappyness = 0.95
        gaps = 0.9
        parsimony_informative = False
        constant_site = True

        assert False == shouldKeep(
            mode, parsimony_informative, constant_site, gappyness, gaps
        )

    def test_gappy_mode(self):
        ## setup
        gappyness = 0.00
        parsimony_informative = True
        keepD = {}
        trimD = {}
        i = 2
        gaps = 0.9
        alignment = AlignIO.read(f"{here.parent}/examples/simple.fa", "fasta")
        use_log = False
        constant_site = False

        for entry in alignment:
            keepD[entry.description] = np.empty([6], dtype=str)
        trimD = {}
        for entry in alignment:
            trimD[entry.description] = np.empty([6], dtype=str)

        ## execution
        keepD, trimD = trim(
            gappyness,
            parsimony_informative,
            constant_site,
            keepD,
            trimD,
            i,
            gaps,
            alignment,
            TrimmingMode.gappy,
            use_log,
        )

        ## check results
        expected_keepD = {
            "1": np.array(["", "", "G", "", "", ""]),
            "2": np.array(["", "", "G", "", "", ""]),
            "3": np.array(["", "", "G", "", "", ""]),
            "4": np.array(["", "", "A", "", "", ""]),
            "5": np.array(["", "", "a", "", "", ""]),
        }
        expected_trimD = {
            "1": np.array(["", "", "", "", "", ""]),
            "2": np.array(["", "", "", "", "", ""]),
            "3": np.array(["", "", "", "", "", ""]),
            "4": np.array(["", "", "", "", "", ""]),
            "5": np.array(["", "", "", "", "", ""]),
        }

        assert expected_keepD.keys() == keepD.keys()
        assert all(
            np.array_equal(expected_keepD[key], keepD[key]) for key in expected_keepD
        )
        assert expected_trimD.keys() == trimD.keys()
        assert all(
            np.array_equal(expected_trimD[key], trimD[key]) for key in expected_trimD
        )

    def test_kpi_gappy_mode(self):
        ## setup
        gappyness = 0.6
        parsimony_informative = False
        constant_site = True
        keepD = {}
        trimD = {}
        i = 1
        gaps = 0.9
        alignment = AlignIO.read(f"{here.parent}/examples/simple.fa", "fasta")
        use_log = False

        for entry in alignment:
            keepD[entry.description] = np.empty([6], dtype=str)
        trimD = {}
        for entry in alignment:
            trimD[entry.description] = np.empty([6], dtype=str)

        ## execution
        keepD, trimD = trim(
            gappyness,
            parsimony_informative,
            constant_site,
            keepD,
            trimD,
            i,
            gaps,
            alignment,
            TrimmingMode.kpi_gappy,
            use_log,
        )

        ## check results
        expected_keepD = {
            "1": np.array(["", "", "", "", "", ""]),
            "2": np.array(["", "", "", "", "", ""]),
            "3": np.array(["", "", "", "", "", ""]),
            "4": np.array(["", "", "", "", "", ""]),
            "5": np.array(["", "", "", "", "", ""]),
        }
        expected_trimD = {
            "1": np.array(["", "-", "", "", "", ""]),
            "2": np.array(["", "-", "", "", "", ""]),
            "3": np.array(["", "-", "", "", "", ""]),
            "4": np.array(["", "G", "", "", "", ""]),
            "5": np.array(["", "C", "", "", "", ""]),
        }

        assert expected_keepD.keys() == keepD.keys()
        assert all(
            np.array_equal(expected_keepD[key], keepD[key]) for key in expected_keepD
        )
        assert expected_trimD.keys() == trimD.keys()
        assert all(
            np.array_equal(expected_trimD[key], trimD[key]) for key in expected_trimD
        )

    def test_kpi_mode(self):
        ## setup
        gappyness = 0.2
        parsimony_informative = True
        constant_site = False
        keepD = {}
        trimD = {}
        i = 5
        gaps = 0.9
        alignment = AlignIO.read(f"{here.parent}/examples/simple.fa", "fasta")
        use_log = False

        for entry in alignment:
            keepD[entry.description] = np.empty([6], dtype=str)
        trimD = {}
        for entry in alignment:
            trimD[entry.description] = np.empty([6], dtype=str)

        ## execution
        keepD, trimD = trim(
            gappyness,
            parsimony_informative,
            constant_site,
            keepD,
            trimD,
            i,
            gaps,
            alignment,
            TrimmingMode.kpi,
            use_log,
        )

        ## check results
        expected_keepD = {
            "1": np.array(["", "", "", "", "", "T"]),
            "2": np.array(["", "", "", "", "", "T"]),
            "3": np.array(["", "", "", "", "", "A"]),
            "4": np.array(["", "", "", "", "", "A"]),
            "5": np.array(["", "", "", "", "", "-"]),
        }
        expected_trimD = {
            "1": np.array(["", "", "", "", "", ""]),
            "2": np.array(["", "", "", "", "", ""]),
            "3": np.array(["", "", "", "", "", ""]),
            "4": np.array(["", "", "", "", "", ""]),
            "5": np.array(["", "", "", "", "", ""]),
        }

        assert expected_keepD.keys() == keepD.keys()
        assert all(
            np.array_equal(expected_keepD[key], keepD[key]) for key in expected_keepD
        )
        assert expected_trimD.keys() == trimD.keys()
        assert all(
            np.array_equal(expected_trimD[key], trimD[key]) for key in expected_trimD
        )

    def test_kpic_mode(self):
        ## setup
        gappyness = 0.2
        parsimony_informative = False
        constant_site = True
        keepD = {}
        trimD = {}
        i = 0
        gaps = 0.9
        alignment = AlignIO.read(f"{here.parent}/examples/simple.fa", "fasta")
        use_log = False

        for entry in alignment:
            keepD[entry.description] = np.empty([6], dtype=str)
        trimD = {}
        for entry in alignment:
            trimD[entry.description] = np.empty([6], dtype=str)

        ## execution
        keepD, trimD = trim(
            gappyness,
            parsimony_informative,
            constant_site,
            keepD,
            trimD,
            i,
            gaps,
            alignment,
            TrimmingMode.kpic,
            use_log,
        )

        ## check results
        expected_keepD = {
            "1": np.array(["A", "", "", "", "", ""]),
            "2": np.array(["A", "", "", "", "", ""]),
            "3": np.array(["A", "", "", "", "", ""]),
            "4": np.array(["A", "", "", "", "", ""]),
            "5": np.array(["A", "", "", "", "", ""]),
        }
        expected_trimD = {
            "1": np.array(["", "", "", "", "", ""]),
            "2": np.array(["", "", "", "", "", ""]),
            "3": np.array(["", "", "", "", "", ""]),
            "4": np.array(["", "", "", "", "", ""]),
            "5": np.array(["", "", "", "", "", ""]),
        }

        assert expected_keepD.keys() == keepD.keys()
        assert all(
            np.array_equal(expected_keepD[key], keepD[key]) for key in expected_keepD
        )
        assert expected_trimD.keys() == trimD.keys()
        assert all(
            np.array_equal(expected_trimD[key], trimD[key]) for key in expected_trimD
        )

    def test_kpic_gappy_mode(self):
        ## setup
        gappyness = 0.2
        parsimony_informative = False
        constant_site = False
        keepD = {}
        trimD = {}
        i = 3
        gaps = 0.9
        alignment = AlignIO.read(f"{here.parent}/examples/simple.fa", "fasta")
        use_log = False

        for entry in alignment:
            keepD[entry.description] = np.empty([6], dtype=str)
        trimD = {}
        for entry in alignment:
            trimD[entry.description] = np.empty([6], dtype=str)

        ## execution
        keepD, trimD = trim(
            gappyness,
            parsimony_informative,
            constant_site,
            keepD,
            trimD,
            i,
            gaps,
            alignment,
            TrimmingMode.kpic_gappy,
            use_log,
        )

        ## check results
        expected_keepD = {
            "1": np.array(["", "", "", "", "", ""]),
            "2": np.array(["", "", "", "", "", ""]),
            "3": np.array(["", "", "", "", "", ""]),
            "4": np.array(["", "", "", "", "", ""]),
            "5": np.array(["", "", "", "", "", ""]),
        }
        expected_trimD = {
            "1": np.array(["", "", "", "T", "", ""]),
            "2": np.array(["", "", "", "-", "", ""]),
            "3": np.array(["", "", "", "-", "", ""]),
            "4": np.array(["", "", "", "-", "", ""]),
            "5": np.array(["", "", "", "-", "", ""]),
        }

        assert expected_keepD.keys() == keepD.keys()
        assert all(
            np.array_equal(expected_keepD[key], keepD[key]) for key in expected_keepD
        )
        assert expected_trimD.keys() == trimD.keys()
        assert all(
            np.array_equal(expected_trimD[key], trimD[key]) for key in expected_trimD
        )