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

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/clipkit_repo/tests/unit/test_modes.py	Fri Mar 25 13:04:31 2022 +0000
@@ -0,0 +1,415 @@
+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
+        )