diff clipkit_repo/tests/unit/test_smart_gap_helper.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_smart_gap_helper.py	Fri Mar 25 13:04:31 2022 +0000
@@ -0,0 +1,158 @@
+import pytest
+import pytest_mock
+from pathlib import Path
+
+
+import numpy as np
+from Bio import AlignIO
+from Bio import SeqIO
+from Bio.Seq import Seq
+from Bio.SeqRecord import SeqRecord
+from Bio.Align import MultipleSeqAlignment
+
+from clipkit.smart_gap_helper import (
+    smart_gap_threshold_determination,
+    greatest_diff_in_slopes,
+    gap_to_gap_slope, 
+    get_gaps_distribution,
+    count_and_sort_gaps
+)
+from clipkit.files import FileFormat
+
+here = Path(__file__)
+
+class TestSmartGapsHelper(object):
+    def test_smart_gap_threshold_simple_case(self):
+        ## set up
+        alignment = AlignIO.read(f"{here.parent}/examples/simple.fa", "fasta")
+        expected_gaps = 0.8
+
+        ## execution
+        gaps = smart_gap_threshold_determination(alignment)
+
+        ## check results
+        assert expected_gaps == gaps
+
+    def test_smart_gap_threshold_standard_case(self):
+        ## set up
+        alignment = AlignIO.read(f"{here.parent}/examples/EOG091N44M8_aa.fa", "fasta")
+        
+        ## execution
+        gaps = smart_gap_threshold_determination(alignment)
+        expected_gaps = 0.8803
+
+        ## check results
+        assert expected_gaps == gaps
+
+    def test_greatest_diff_in_slopes_simple_case(self):
+        ## set up
+        slopes = [0.833333333333333]
+        gaps_arr = [[0.8, 1.0], [0.6, 1.0], [0.2, 1.0], [0.0, 3.0]]
+        expected_return = 0.8
+
+        ## execution
+        greatest_diff = greatest_diff_in_slopes(slopes, gaps_arr)
+
+        ## check results
+        assert greatest_diff == expected_return
+
+    def test_greatest_diff_in_slopes_standard_case(self):
+        ## set up
+        slopes = [
+            0.453329706695677,
+            0.1903630604288502,
+            2.153316106804466,
+            0.11466574934067258,
+            2.4933133868262236,
+            0.6879944960440355,
+            0.037924469626292194,
+            2.1786492374727793,
+            2.4933133868262236,
+            4.12796697626421,
+            1.6999864001087854,
+            1.0319917440660464,
+            0.7933269867174482,
+            0.11399518940300717,
+            0.8026602453847114
+        ]
+        gaps_arr = [
+            [0.9915, 136.0],
+            [0.9829, 4.0],
+            [0.9573, 5.0],
+            [0.9487, 19.0],
+            [0.9402, 1.0],
+            [0.9316, 22.0],
+            [0.9231, 6.0],
+            [0.8974, 1.0],
+            [0.8889, 19.0],
+            [0.8803, 22.0],
+            [0.8718, 36.0],
+            [0.8632, 15.0],
+            [0.8462, 18.0],
+            [0.8376, 7.0],
+            [0.8205, 2.0],
+            [0.812, 7.0],
+            [0.8034, 19.0],
+            [0.7949, 1.0],
+            [0.7692, 288.0],
+            [0.7607, 279.0],
+            [0.7521, 6.0],
+            [0.6667, 5.0],
+            [0.1197, 1.0],
+            [0.1026, 2.0],
+            [0.0855, 1.0],
+            [0.0769, 1.0],
+            [0.0598, 2.0],
+            [0.0342, 1.0],
+            [0.0256, 3.0],
+            [0.0171, 1.0],
+            [0.0085, 1.0],
+            [0.0, 95.0]
+        ]
+        expected_return = 0.8803
+
+        ## execution
+        greatest_diff = greatest_diff_in_slopes(slopes, gaps_arr)
+
+        ## check results
+        assert greatest_diff == expected_return
+
+    def test_gap_to_gap_slope_simple_case(self):
+        ## set up
+        gaps_arr = [[0.8, 1.0], [0.6, 1.0], [0.2, 1.0], [0.0, 3.0]]
+        alignment_length = 6
+
+        ## execution
+        slopes = gap_to_gap_slope(gaps_arr, alignment_length)
+        expected_slopes = [0.833333333333333]
+
+        ## check results
+        assert expected_slopes == slopes
+
+    def test_get_gaps_distribution(self):
+        ## set up
+        alignment = AlignIO.read(f"{here.parent}/examples/simple.fa", "fasta")
+        alignment_length = 6
+
+        ## execution
+        gaps_arr = get_gaps_distribution(alignment, alignment_length)
+        expected_gaps_arr = [0.0, 0.6, 0.0, 0.8, 0.0, 0.2]
+
+        ## check results
+        assert expected_gaps_arr == gaps_arr
+
+    def test_count_and_sort_gaps(self):
+        ## set up
+        gaps_dist = [0.0, 0.6, 0.0, 0.8, 0.0, 0.2]
+
+        ## execution
+        gaps_arr = count_and_sort_gaps(gaps_dist)
+        expected_gaps_arr = [[0.8, 1.0], [0.6, 1.0], [0.2, 1.0], [0.0, 3.0]]
+
+        ## check results
+        assert expected_gaps_arr == gaps_arr
+
+
+        
+
+