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

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"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
author padge
date Fri, 25 Mar 2022 13:04:31 +0000
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1 import pytest
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2 import pytest_mock
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3 from pathlib import Path
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6 import numpy as np
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7 from Bio import AlignIO
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8 from Bio import SeqIO
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9 from Bio.Seq import Seq
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10 from Bio.SeqRecord import SeqRecord
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11 from Bio.Align import MultipleSeqAlignment
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13 from clipkit.helpers import count_characters_at_position
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14 from clipkit.helpers import get_sequence_at_position_and_report_features
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15 from clipkit.helpers import parsimony_informative_or_constant
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16 from clipkit.helpers import populate_empty_keepD_and_trimD
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17 from clipkit.helpers import join_keepD_and_trimD
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18 from clipkit.helpers import write_trimD
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19 from clipkit.helpers import write_keepD
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20 from clipkit.files import FileFormat
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22 here = Path(__file__)
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25 @pytest.fixture
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26 def sample_msa():
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27 return MultipleSeqAlignment(
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28 [
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29 SeqRecord(
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30 seq=Seq("['A']"),
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31 id="1",
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32 name="<unknown name>",
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33 description="",
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34 dbxrefs=[],
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35 ),
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36 SeqRecord(
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37 seq=Seq("['A']"),
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38 id="2",
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39 name="<unknown name>",
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40 description="",
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41 dbxrefs=[],
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42 ),
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43 SeqRecord(
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44 seq=Seq("['A']"),
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45 id="3",
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46 name="<unknown name>",
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47 description="",
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48 dbxrefs=[],
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49 ),
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50 SeqRecord(
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51 seq=Seq("['A']"),
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52 id="4",
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53 name="<unknown name>",
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54 description="",
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55 dbxrefs=[],
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56 ),
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57 SeqRecord(
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58 seq=Seq("['A']"),
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59 id="5",
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60 name="<unknown name>",
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61 description="",
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62 dbxrefs=[],
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63 ),
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64 ]
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65 )
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66
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67
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68 class TestCountCharactersAtPosition(object):
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69 def test_gives_count_for_each_char(self):
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70 ## setup
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71 s = "ACTTTGGG"
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72
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73 ## execution
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74 res = count_characters_at_position(s)
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75
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76 ## check results
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77 # test that each character has an associated key
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78 for char in s:
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79 assert char in res.keys()
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80
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81 # test that the len of the res is equal to the
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82 # number of unique string characters
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83 assert len(res) == len(set(s))
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84
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85
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86 class TestGetSequenceAtPositionAndReportFeatures(object):
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87 def test_gets_sequence_and_gappyness(self):
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88 ## setup
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89 alignment = AlignIO.read(f"{here.parent}/examples/simple.fa", "fasta")
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90 i = int(5)
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91
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92 ## execution
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93 seq, gappyness = get_sequence_at_position_and_report_features(alignment, i)
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94
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95 ## check results
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96 # test output types
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97 assert isinstance(seq, str)
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98 assert isinstance(gappyness, float)
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101 class TestParsimonyInformativeOrConstant(object):
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102 def test_parsimony_informative_or_constant(self):
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103 ## set up
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104 # pi = parsimony informative
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105 num_occurences_pi = {"A": 5, "T": 10, "G": 2, "C": 4}
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106 # npi = not parsimony informative
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107 num_occurences_npi = {"A": 1, "T": 10, "G": 1}
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108 # Const = constant
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109 num_occurences_const = {"A": 10}
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110 # nConst = not constant
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111 num_occurences_nconst = {"A": 1}
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112
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113 ## execution
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114 # result is True and False
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115 (
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116 is_parsimony_informative,
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117 constant_site_holder_is_pi,
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118 ) = parsimony_informative_or_constant(num_occurences_pi)
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119 # result is False and False
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120 (
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121 is_not_parsimony_informative,
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122 constant_site_holder_is_npi,
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123 ) = parsimony_informative_or_constant(num_occurences_npi)
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124 # result is False and True
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125 is_not_pi_0, is_constant_site = parsimony_informative_or_constant(
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126 num_occurences_const
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127 )
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128 # result is False and False
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129 is_not_pi_1, is_not_constant_site = parsimony_informative_or_constant(
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130 num_occurences_nconst
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131 )
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132
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133 ## check results
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134 assert is_parsimony_informative == True and constant_site_holder_is_pi == False
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135 assert (
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136 is_not_parsimony_informative == False
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137 and constant_site_holder_is_npi == False
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138 )
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139 assert is_not_pi_0 == False and is_constant_site == True
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140 assert is_not_pi_1 == False and is_not_constant_site == False
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141
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142
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143 class TestPopulateEmptyKeepDAndTrimD(object):
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144 def test_populate_empty_keepD_and_trimD(self):
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145 ## set up
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146 alignment = AlignIO.read(f"{here.parent}/examples/simple.fa", "fasta")
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147
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148 ## execution
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149 keepD, trimD = populate_empty_keepD_and_trimD(alignment)
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150
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151 ## check results
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152 expected_keepD = {
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153 "1": np.zeros([6], dtype=bytes),
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154 "2": np.zeros([6], dtype=bytes),
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155 "3": np.zeros([6], dtype=bytes),
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156 "4": np.zeros([6], dtype=bytes),
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157 "5": np.zeros([6], dtype=bytes),
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158 }
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159 expected_trimD = {
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160 "1": np.zeros([6], dtype=bytes),
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161 "2": np.zeros([6], dtype=bytes),
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162 "3": np.zeros([6], dtype=bytes),
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163 "4": np.zeros([6], dtype=bytes),
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164 "5": np.zeros([6], dtype=bytes),
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165 }
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166
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167 assert expected_keepD.keys() == keepD.keys()
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168 assert all(
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169 np.array_equal(expected_keepD[key], keepD[key]) for key in expected_keepD
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170 )
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171 assert expected_trimD.keys() == trimD.keys()
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172 assert all(
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173 np.array_equal(expected_trimD[key], trimD[key]) for key in expected_trimD
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174 )
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175
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176
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177 class TestJoinKeepDAndTrimD(object):
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178 def test_join_keepD_and_trimD(self):
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179 ## set up
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180
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181 keepD = {
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182 '1': np.array([b'A', b'-', b'G', b'T', b'A', b'T'], dtype='|S1'),
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183 '2': np.array([b'A', b'-', b'G', b'-', b'A', b'T'], dtype='|S1'),
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184 '3': np.array([b'A', b'-', b'G', b'-', b'T', b'A'], dtype='|S1'),
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185 '4': np.array([b'A', b'G', b'A', b'-', b'T', b'A'], dtype='|S1'),
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186 '5': np.array([b'A', b'C', b'a', b'-', b'T', b'-'], dtype='|S1')
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187 }
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188
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189 trimD = {
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190 '1': np.array([b'', b'', b'', b'', b'', b''], dtype='|S1'),
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191 '2': np.array([b'', b'', b'', b'', b'', b''], dtype='|S1'),
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192 '3': np.array([b'', b'', b'', b'', b'', b''], dtype='|S1'),
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193 '4': np.array([b'', b'', b'', b'', b'', b''], dtype='|S1'),
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194 '5': np.array([b'', b'', b'', b'', b'', b''], dtype='|S1')
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195 }
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196
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197 ## execution
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198 keepD, trimD = join_keepD_and_trimD(keepD, trimD)
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199
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200 ## check results
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201 expected_keepD = {
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202 "1": "A-GTAT",
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203 "2": "A-G-AT",
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204 "3": "A-G-TA",
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205 "4": "AGA-TA",
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206 "5": "ACa-T-",
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207 }
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208 expected_trimD = {"1": "", "2": "", "3": "", "4": "", "5": ""}
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209
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210 assert expected_keepD == keepD
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211 assert expected_trimD == trimD
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212
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213
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214 class TestWriteKeepD(object):
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215 def test_write_keepD_writes_file(self, mocker, sample_msa):
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216 ## set up
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217 keepD = {"1": ["A"], "2": ["A"], "3": ["A"], "4": ["A"], "5": ["A"]}
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218 out_file = "output_file_name.fa"
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219 out_file_format = FileFormat.fasta
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220 mock_msa = mocker.patch("clipkit.helpers.MultipleSeqAlignment")
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221 mock_msa.return_value = sample_msa
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222 mock_write = mocker.patch("clipkit.helpers.SeqIO.write")
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223
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224 ## execution
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225 write_keepD(keepD, out_file, out_file_format)
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226
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227 ## check results
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228 mock_write.assert_called_once_with(sample_msa, out_file, out_file_format.value)
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229
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230
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231 class TestWriteTrimD(object):
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232 def test_write_trimD_calls_seqio_write(self, mocker, sample_msa):
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233 ## set up
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234 trimD = {"1": ["A"], "2": ["A"], "3": ["A"], "4": ["A"], "5": ["A"]}
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235 out_file = "output_file_name.fa"
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236 out_file_format = FileFormat.fasta
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237 mock_msa = mocker.patch("clipkit.helpers.MultipleSeqAlignment")
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238 mock_msa.return_value = sample_msa
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239 mock_write = mocker.patch("Bio.SeqIO.write")
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240
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241 ## execution
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242 write_trimD(trimD, out_file, out_file_format)
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243
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244 ## check results
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245 expected_completmentOut = f"{out_file}.complement"
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246 mock_write.assert_called_once_with(
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247 sample_msa, expected_completmentOut, out_file_format.value
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248 )