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How to use testCoverageDetection method in green

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test_coverage_detection.py

Source:test_coverage_detection.py

1import sys2import math3import csv4import os5import unittest6from io import StringIO7sys.path.append(".")8import annogesiclib.coverage_detection as cover_detect9from mock_args_container import MockClass10class Mock_func(object):11    def mock_check_tex(self, template_texs, covers, target_datas, cutoff,12                       tex_notex, poss, type_, notex, median,13                       coverages, utr_type):14        for srna in Example().cover_datas:15            target_datas.append(srna)16        poss["start"] = 10017        poss["end"] = 20218        return 219class TestCoverageDetection(unittest.TestCase):20    def setUp(self):21        self.example = Example()22        self.mock_args = MockClass()23    def test_coverage_comparison_first(self):24        first = True25        cover_sets = {"high": -1, "low": -1}26        poss = {"high": -1, "low": -1}27        cover = 10028        cover_detect.coverage_comparison(29            cover, cover_sets, poss, first, "+", 50)30        self.assertDictEqual(cover_sets, {"high": 100, "low": 100})31        self.assertDictEqual(poss, {"high": 50, "low": 50})32        33    def test_coverage_comparison_forward(self):34        first = False35        cover_sets = {"high": 50, "low": 20}36        poss = {"high": 10, "low": 30}37        cover = 10038        cover_detect.coverage_comparison(39            cover, cover_sets, poss, first, "+", 50)40        self.assertDictEqual(cover_sets, {"high": 100, "low": 100})41        self.assertDictEqual(poss, {"high": 50, "low": 50})42        cover = 3043        cover_detect.coverage_comparison(44            cover, cover_sets, poss, first, "+", 51)45        self.assertDictEqual(cover_sets, {"high": 100, "low": 30})46        self.assertDictEqual(poss, {"high": 50, "low": 51})47    def test_coverage_comparison_reverse(self):48        first = False49        cover_sets = {"high": 50, "low": 20}50        poss = {"high": 30, "low": 10}51        cover = 10052        cover_detect.coverage_comparison(53            cover, cover_sets, poss, first, "-", 50)54        self.assertDictEqual(cover_sets, {"high": 100, "low": 100})55        self.assertDictEqual(poss, {"high": 50, "low": 50})56        cover = 3057        cover_detect.coverage_comparison(58            cover, cover_sets, poss, first, "-", 49)59        self.assertDictEqual(cover_sets, {"high": 100, "low": 30})60        self.assertDictEqual(poss, {"high": 50, "low": 49})61    def test_define_cutoff_median(self):62        coverages = {"3utr": "mean", "5utr": "median"}63        median = {"track_a": {"median": 100, "mean": 200},64                  "track_b": {"median": 30, "mean": 80}}65        cutoff = cover_detect.define_cutoff(coverages, median, "5utr")66        self.assertDictEqual(cutoff, {'track_a': 100, 'track_b': 30})67        cutoff = cover_detect.define_cutoff(coverages, median, "3utr")68        self.assertDictEqual(cutoff, {'track_a': 200, 'track_b': 80})69    def test_check_tex(self):70        template_texs = self.example.texs71        covers = self.example.cover_datas72        coverages = {"3utr": 100, "5utr": 600}73        poss = {"high": 30, "low": 10}74        median = {"track1_tex": {"median": 100, "mean": 200},75                  "track1_notex": {"median": 30, "mean": 80},76                  "track2_tex": {"median": 150, "mean": 200},77                  "track2_notex": {"median": 10, "mean": 20},78                  "frag": {"median": 80, "mean": 100}}79        target_datas = []80        texs = {"track1_tex@AND@track1_notex": 0,81                "track2_tex@AND@track2_notex": 0}82        detect_num_lib = cover_detect.check_tex(83            template_texs, covers, target_datas, 20, None, poss, median,84            coverages, "3utr", 200, 2)85        self.assertEqual(detect_num_lib, 2)86        num_frag = 087        num_tex = 088        for target in target_datas:89            if target["type"] == "frag":90                num_frag += 191            else:92                num_tex += 193        self.assertEqual(num_frag, 1)94        self.assertEqual(num_tex, 2)95        detect_num_lib = cover_detect.check_tex(96            template_texs, covers, target_datas, 20, "sRNA_utr_derived",97            poss, median, coverages, "5utr", 200, 2)98        self.assertEqual(detect_num_lib, 2)99        self.assertDictEqual(poss, {100            'start': 100, 'high': 30, 'end': 202, 'low': 10})101    def test_replicate_comparison(self):102        cover_detect.check_tex = Mock_func().mock_check_tex103        template_texs = self.example.texs104        srna_covers = {"texnotex": self.example.cover_datas}105        coverages = {"3utr": 100, "5utr": 600}106        median = {"track1_tex": {"median": 100, "mean": 200},107                  "track1_notex": {"median": 30, "mean": 80},108                  "track2_tex": {"median": 150, "mean": 200},109                  "track2_notex": {"median": 10, "mean": 20},110                  "frag": {"median": 80, "mean": 100}}111        texs = {"track1_tex@AND@track1_notex": 0,112                "track2_tex@AND@track2_notex": 0}113        args = self.mock_args.mock()114        args.replicates = {"tex": ["all_2"], "frag": ["all_1"]}115        args.tex_notex = 2116        srna_datas = cover_detect.replicate_comparison(args, srna_covers, "+",117                     "sRNA_utr_derived", median,118                     coverages, "3utr", 100, 200, template_texs)119        self.assertEqual(srna_datas["best"], 500)120        self.assertEqual(srna_datas["track"], "frag")121        self.assertEqual(srna_datas["high"], 700)122        self.assertEqual(srna_datas["low"], 400)123        self.assertEqual(srna_datas["start"], 100)124        self.assertEqual(srna_datas["end"], 202)125class Example(object):126    cover_datas = [127        {"avg": 300, "type": "tex", "track": "track1_tex",128         "final_start": 100, "final_end": 200, "high": 500, "low": 100},129        {"avg": 300, "type": "notex", "track": "track1_notex",130         "final_start": 100, "final_end": 200, "high": 500, "low": 100},131        {"avg": 10, "type": "tex", "track": "track2_tex",132         "final_start": 101, "final_end": 200, "high": 50, "low": 0},133        {"avg": 10, "type": "notex", "track": "track2_notex",134         "final_start": 101, "final_end": 200, "high": 50, "low": 0},135        {"avg": 500, "type": "frag", "track": "frag",136         "final_start": 100, "final_end": 202, "high": 700, "low": 400}]137    texs = {"track1_tex_track1_notex": 0,138            "track2_tex_track2_notex": 0}139    cutoff = {"track1_tex": 200, "track1_notex": 200,140              "track2_tex": 200, "track2_notex": 200,141              "frag": 200}142if __name__ == "__main__":...

test_output.py

Source:test_output.py

...150        gs = GreenStream(s)151        gs.write = MagicMock()152        gs.writelines(["one", "two", "three"])153        self.assertEqual(len(gs.write.mock_calls), 3)154    def testCoverageDetection(self):155        """156        write() detects a coverage percentage flying by157        """158        s = StringIO()159        gs = GreenStream(s)160        gs.write(161            "\n---------------------------------------------------\nTOTAL                   896    367    59%\nRan"162        )163        self.assertEqual(gs.coverage_percent, 59)164    def testEncodingMirrors(self):165        """166        The encoding of a stream gets mirrored through167        """168        s = StringIO()...

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