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annotate clipkit_repo/tests/integration/test_kpi_mode.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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49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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1 import pytest
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2 from pathlib import Path
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4 from clipkit.clipkit import execute
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5 from clipkit.files import FileFormat
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6 from clipkit.modes import TrimmingMode
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8 here = Path(__file__)
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11 @pytest.mark.integration
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12 class TestKpiMode(object):
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13 def test_simple(self):
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14 """
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15 usage: clipkit simple.fa -kpi
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16 """
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17 input_file = f"{here.parent}/samples/simple.fa"
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18 output_file = "output/simpla.fa.TestKpiMode_test_simple.clipkit"
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20 kwargs = dict(
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21 input_file=input_file,
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22 output_file=output_file,
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23 input_file_format='fasta',
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24 output_file_format='fasta',
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25 complement=False,
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26 gaps=0.9,
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27 mode=TrimmingMode.kpi,
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28 use_log=False,
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29 )
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30 execute(**kwargs)
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32 with open(f"{here.parent}/expected/simple.fa_kpi", "r") as expected:
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33 expected_content = expected.read()
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34
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35 with open(output_file, "r") as out_file:
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36 output_content = out_file.read()
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37
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38 assert expected_content == output_content
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39
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40 def test_simple_long_description(self):
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41 """
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42 usage: clipkit simple.fa -kpi
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43 """
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44 input_file = f"{here.parent}/samples/simple_long_description.fa"
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45 output_file = "output/simple_long_description.fa.TestKpiMode_test_simple.clipkit"
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46
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47 kwargs = dict(
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48 input_file=input_file,
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49 output_file=output_file,
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50 input_file_format='fasta',
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51 output_file_format='fasta',
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52 complement=False,
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53 gaps=0.9,
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54 mode=TrimmingMode.kpi,
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55 use_log=False,
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56 )
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57 execute(**kwargs)
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58
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59 with open(f"{here.parent}/expected/simple_long_description.fa_kpi", "r") as expected:
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60 expected_content = expected.read()
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61
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62 with open(output_file, "r") as out_file:
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63 output_content = out_file.read()
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64
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65 assert expected_content == output_content
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66
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67 def test_12_YIL115C_Anc_2_253_codon_aln(self):
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68 """
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69 test kpi with codon alignment of yeast sequences
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70 usage: clipkit 12_YIL115C_Anc_2.253_codon_aln.fasta -m kpi
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71 """
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72 input_file = f"{here.parent}/samples/12_YIL115C_Anc_2.253_codon_aln.fasta"
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73 output_file = "output/12_YIL115C_Anc_2.253_codon_aln.fasta.clipkit"
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74
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75 kwargs = dict(
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76 input_file=input_file,
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77 output_file=output_file,
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78 input_file_format='fasta',
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79 output_file_format='fasta',
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80 complement=False,
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81 gaps=0.9,
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82 mode=TrimmingMode.kpi,
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83 use_log=False,
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84 )
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85 execute(**kwargs)
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86
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87 with open(
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88 f"{here.parent}/expected/12_YIL115C_Anc_2.253_codon_aln.fasta_kpi", "r"
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89 ) as expected:
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90 expected_content = expected.read()
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91
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92 with open(output_file, "r") as out_file:
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93 output_content = out_file.read()
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94
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95 assert expected_content == output_content
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96
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97 def test_12_YIL115C_Anc_2_253_aa_aln(self):
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98 """
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99 test kpi with amino acid alignment of yeast sequences
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100 usage: clipkit 12_YIL115C_Anc_2.253_aa_aln.fasta -m kpi
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101 """
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102 input_file = f"{here.parent}/samples/12_YIL115C_Anc_2.253_aa_aln.fasta"
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103 output_file = "output/12_YIL115C_Anc_2.253_aa_aln.fasta.clipkit"
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104
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105 kwargs = dict(
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106 input_file=input_file,
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107 output_file=output_file,
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108 input_file_format='fasta',
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109 output_file_format='fasta',
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110 complement=False,
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111 gaps=0.9,
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112 mode=TrimmingMode.kpi,
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113 use_log=False,
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114 )
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115 execute(**kwargs)
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116
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117 with open(
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118 f"{here.parent}/expected/12_YIL115C_Anc_2.253_aa_aln.fasta_kpi", "r"
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119 ) as expected:
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120 expected_content = expected.read()
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121
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122 with open(output_file, "r") as out_file:
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123 output_content = out_file.read()
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124
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125 assert expected_content == output_content
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126
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127 def test_24_ENSG00000163519_aa_aln(self):
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128 """
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129 test kpi with amino acid alignment of mammalian sequences
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130 usage: clipkit 24_ENSG00000163519_aa_aln.fasta -m kpi
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131 """
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132 input_file = f"{here.parent}/samples/24_ENSG00000163519_aa_aln.fasta"
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133 output_file = "output/24_ENSG00000163519_aa_aln.fasta.clipkit"
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134
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135 kwargs = dict(
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136 input_file=input_file,
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137 output_file=output_file,
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138 input_file_format='fasta',
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139 output_file_format='fasta',
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140 complement=False,
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141 gaps=0.9,
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142 mode=TrimmingMode.kpi,
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143 use_log=False,
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144 )
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145 execute(**kwargs)
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146
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147 with open(
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148 f"{here.parent}/expected/24_ENSG00000163519_aa_aln.fasta_kpi", "r"
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149 ) as expected:
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150 expected_content = expected.read()
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151
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152 with open(output_file, "r") as out_file:
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153 output_content = out_file.read()
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154
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155 assert expected_content == output_content
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156
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157 def test_24_ENSG00000163519_codon_aln(self):
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158 """
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159 test kpi with codon alignment of mammalian sequences
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160 usage: clipkit 24_ENSG00000163519_codon_aln.fasta -m kpi
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161 """
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162 input_file = f"{here.parent}/samples/24_ENSG00000163519_codon_aln.fasta"
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163 output_file = "output/24_ENSG00000163519_codon_aln.fasta.clipkit"
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164
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165 kwargs = dict(
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166 input_file=input_file,
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167 output_file=output_file,
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168 input_file_format='fasta',
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169 output_file_format='fasta',
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170 complement=False,
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171 gaps=0.9,
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172 mode=TrimmingMode.kpi,
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173 use_log=False,
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174 )
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175 execute(**kwargs)
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176
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177 with open(
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178 f"{here.parent}/expected/24_ENSG00000163519_codon_aln.fasta_kpi", "r"
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179 ) as expected:
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180 expected_content = expected.read()
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181
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182 with open(output_file, "r") as out_file:
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183 output_content = out_file.read()
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184
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185 assert expected_content == output_content
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186
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187 def test_EOG091N44M8_aa(self):
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188 """
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189 test kpi with amino acid alignment of Penicillium sequences
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190 usage: clipkit EOG091N44M8_aa.fa -m kpi
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191 """
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192 input_file = f"{here.parent}/samples/EOG091N44M8_aa.fa"
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193 output_file = "output/EOG091N44M8_aa.fa.clipkit"
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194
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195 kwargs = dict(
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196 input_file=input_file,
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197 output_file=output_file,
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198 input_file_format='fasta',
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199 output_file_format='fasta',
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200 complement=False,
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201 gaps=0.9,
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202 mode=TrimmingMode.kpi,
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203 use_log=False,
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204 )
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205 execute(**kwargs)
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206
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207 with open(f"{here.parent}/expected/EOG091N44M8_aa.fa_kpi", "r") as expected:
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208 expected_content = expected.read()
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209
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210 with open(output_file, "r") as out_file:
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211 output_content = out_file.read()
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212
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213 assert expected_content == output_content
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214
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215 def test_EOG091N44M8_nt(self):
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216 """
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217 test kpi with nucleotide alignment of Penicillium sequences
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218 usage: clipkit EOG091N44M8_nt.fa -m kpi
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219 """
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220 input_file = f"{here.parent}/samples/EOG091N44M8_nt.fa"
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221 output_file = "output/EOG091N44M8_nt.fa.clipkit"
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222
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223 kwargs = dict(
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224 input_file=input_file,
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225 output_file=output_file,
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226 input_file_format='fasta',
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227 output_file_format='fasta',
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228 complement=False,
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229 gaps=0.9,
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230 mode=TrimmingMode.kpi,
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231 use_log=False,
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232 )
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233 execute(**kwargs)
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234
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235 with open(f"{here.parent}/expected/EOG091N44M8_nt.fa_kpi", "r") as expected:
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236 expected_content = expected.read()
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237
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238 with open(output_file, "r") as out_file:
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239 output_content = out_file.read()
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240
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241 assert expected_content == output_content
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242
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243 @pytest.mark.slow
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244 def test_EOG092C4VOX_aa(self):
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245 """
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246 test kpi with amino alignment of fungal sequences
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247 usage: clipkit EOG092C4VOX_aa_aln.fasta -m kpi
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248 """
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249 input_file = f"{here.parent}/samples/EOG092C4VOX_aa_aln.fasta"
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250 output_file = "output/EOG092C4VOX_aa_aln.fasta.clipkit"
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251
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252 kwargs = dict(
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253 input_file=input_file,
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254 output_file=output_file,
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255 input_file_format='fasta',
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256 output_file_format='fasta',
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257 complement=False,
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258 gaps=0.9,
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259 mode=TrimmingMode.kpi,
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260 use_log=False,
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261 )
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262 execute(**kwargs)
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263
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264 with open(
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265 f"{here.parent}/expected/EOG092C4VOX_aa_aln.fasta_kpi", "r"
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266 ) as expected:
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267 expected_content = expected.read()
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268
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269 with open(output_file, "r") as out_file:
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270 output_content = out_file.read()
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271
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272 assert expected_content == output_content