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annotate clipkit_repo/tests/integration/test_kpi_gappy_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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3
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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 TestKpiGappyMode(object):
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13 def test_simple(self):
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14 """
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15 usage: clipkit simple.fa -m kpi-gappy
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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.TestKpiGappyMode_test_simple.clipkit"
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19
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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_gappy,
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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_gappy", "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 -m kpi-gappy
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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.clipkit_kpi_gappy"
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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_gappy,
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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_gappy", "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_gappy with codon alignment of yeast sequences
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70 usage: clipkit 12_YIL115C_Anc_2.253_codon_aln.fasta -m kpi-gappy
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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_gappy,
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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_gappy",
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89 "r",
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90 ) as expected:
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91 expected_content = expected.read()
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92
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93 with open(output_file, "r") as out_file:
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94 output_content = out_file.read()
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95
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96 assert expected_content == output_content
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97
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98 def test_12_YIL115C_Anc_2_253_aa_aln(self):
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99 """
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100 test kpi_gappy with amino acid alignment of yeast sequences
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101 usage: clipkit 12_YIL115C_Anc_2.253_aa_aln.fasta -m kpi-gappy
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102 """
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103 input_file = f"{here.parent}/samples/12_YIL115C_Anc_2.253_aa_aln.fasta"
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104 output_file = "output/12_YIL115C_Anc_2.253_aa_aln.fasta.clipkit"
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105
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106 kwargs = dict(
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107 input_file=input_file,
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108 output_file=output_file,
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109 input_file_format='fasta',
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110 output_file_format='fasta',
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111 complement=False,
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112 gaps=0.9,
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113 mode=TrimmingMode.kpi_gappy,
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114 use_log=False,
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115 )
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116 execute(**kwargs)
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117
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118 with open(
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119 f"{here.parent}/expected/12_YIL115C_Anc_2.253_aa_aln.fasta_kpi_gappy", "r"
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120 ) as expected:
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121 expected_content = expected.read()
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122
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123 with open(output_file, "r") as out_file:
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124 output_content = out_file.read()
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125
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126 assert expected_content == output_content
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127
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128 def test_24_ENSG00000163519_aa_aln(self):
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129 """
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130 test kpi_gappy with amino acid alignment of mammalian sequences
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131 usage: clipkit 24_ENSG00000163519_aa_aln.fasta -m kpi-gappy
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132 """
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133 input_file = f"{here.parent}/samples/24_ENSG00000163519_aa_aln.fasta"
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134 output_file = "output/24_ENSG00000163519_aa_aln.fasta.clipkit"
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135
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136 kwargs = dict(
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137 input_file=input_file,
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138 output_file=output_file,
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139 input_file_format='fasta',
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140 output_file_format='fasta',
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141 complement=False,
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142 gaps=0.9,
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143 mode=TrimmingMode.kpi_gappy,
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144 use_log=False,
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145 )
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146 execute(**kwargs)
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147
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148 with open(
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149 f"{here.parent}/expected/24_ENSG00000163519_aa_aln.fasta_kpi_gappy", "r"
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150 ) as expected:
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151 expected_content = expected.read()
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152
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153 with open(output_file, "r") as out_file:
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154 output_content = out_file.read()
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155
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156 assert expected_content == output_content
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157
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158 def test_24_ENSG00000163519_codon_aln(self):
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159 """
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160 test kpi_gappy with codon alignment of mammalian sequences
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161 usage: clipkit 24_ENSG00000163519_codon_aln.fasta -m kpi-gappy
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162 """
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163 input_file = f"{here.parent}/samples/24_ENSG00000163519_codon_aln.fasta"
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164 output_file = "output/24_ENSG00000163519_codon_aln.fasta.clipkit"
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165
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166 kwargs = dict(
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167 input_file=input_file,
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168 output_file=output_file,
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169 input_file_format='fasta',
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170 output_file_format='fasta',
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171 complement=False,
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172 gaps=0.9,
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173 mode=TrimmingMode.kpi_gappy,
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174 use_log=False,
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175 )
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176 execute(**kwargs)
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177
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178 with open(
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179 f"{here.parent}/expected/24_ENSG00000163519_codon_aln.fasta_kpi_gappy", "r"
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180 ) as expected:
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181 expected_content = expected.read()
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182
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183 with open(output_file, "r") as out_file:
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184 output_content = out_file.read()
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185
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186 assert expected_content == output_content
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187
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188 def test_EOG091N44M8_aa(self):
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189 """
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190 test kpi_gappy with amino acid alignment of Penicillium sequences
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191 usage: clipkit EOG091N44M8_aa.fa -m kpi-gappy
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192 """
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193 input_file = f"{here.parent}/samples/EOG091N44M8_aa.fa"
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194 output_file = "output/EOG091N44M8_aa.fa.clipkit"
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195
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196 kwargs = dict(
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197 input_file=input_file,
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198 output_file=output_file,
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199 input_file_format='fasta',
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200 output_file_format='fasta',
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201 complement=False,
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202 gaps=0.9,
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203 mode=TrimmingMode.kpi_gappy,
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204 use_log=False,
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205 )
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206 execute(**kwargs)
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207
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208 with open(
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209 f"{here.parent}/expected/EOG091N44M8_aa.fa_kpi_gappy", "r"
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210 ) as expected:
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211 expected_content = expected.read()
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212
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213 with open(output_file, "r") as out_file:
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214 output_content = out_file.read()
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215
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216 assert expected_content == output_content
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217
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218 def test_EOG091N44M8_nt(self):
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219 """
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220 test kpi_gappy with nucleotide alignment of Penicillium sequences
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221 usage: clipkit EOG091N44M8_nt.fa -m kpi-gappy
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222 """
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223 input_file = f"{here.parent}/samples/EOG091N44M8_nt.fa"
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224 output_file = "output/EOG091N44M8_nt.fa.clipkit"
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225
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226 kwargs = dict(
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227 input_file=input_file,
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228 output_file=output_file,
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229 input_file_format='fasta',
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230 output_file_format='fasta',
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231 complement=False,
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232 gaps=0.9,
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233 mode=TrimmingMode.kpi_gappy,
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234 use_log=False,
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235 )
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236 execute(**kwargs)
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237
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238 with open(
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239 f"{here.parent}/expected/EOG091N44M8_nt.fa_kpi_gappy", "r"
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240 ) as expected:
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241 expected_content = expected.read()
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242
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243 with open(output_file, "r") as out_file:
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244 output_content = out_file.read()
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245
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246 assert expected_content == output_content
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247
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248 @pytest.mark.slow
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249 def test_EOG092C4VOX_aa(self):
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250 """
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251 test gappy with amino alignment of fungal sequences
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252 usage: clipkit EOG092C4VOX_aa_aln.fasta -m kpi-gappy
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253 """
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254 input_file = f"{here.parent}/samples/EOG092C4VOX_aa_aln.fasta"
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255 output_file = "output/EOG092C4VOX_aa_aln.fasta.clipkit"
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256
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257 kwargs = dict(
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258 input_file=input_file,
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259 output_file=output_file,
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260 input_file_format='fasta',
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261 output_file_format='fasta',
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262 complement=False,
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263 gaps=0.9,
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264 mode=TrimmingMode.kpi_gappy,
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265 use_log=False,
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266 )
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267 execute(**kwargs)
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268
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269 with open(
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270 f"{here.parent}/expected/EOG092C4VOX_aa_aln.fasta_kpi_gappy", "r"
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271 ) as expected:
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272 expected_content = expected.read()
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273
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274 with open(output_file, "r") as out_file:
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275 output_content = out_file.read()
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276
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277 assert expected_content == output_content
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278
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279
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280 @pytest.mark.integration
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281 class TestKPIGappyModeCustomGapsParameter(object):
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282 def test_simple(self):
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283 """
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284 test kpi_gappy with a custom gaps parameter
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285 usage: clipkit simple.fa -g 0.2 -m kpi-gappy
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286 """
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287 input_file = f"{here.parent}/samples/simple.fa"
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288 output_file = "output/simpla.fa.clipkit"
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289
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290 kwargs = dict(
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291 input_file=input_file,
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292 output_file=output_file,
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293 input_file_format='fasta',
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294 output_file_format='fasta',
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295 complement=False,
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296 gaps=0.2,
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297 mode=TrimmingMode.kpi_gappy,
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298 use_log=False,
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299 )
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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300 execute(**kwargs)
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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301
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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302 with open(
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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303 f"{here.parent}/expected/simple.fa_kpi_gappy_gaps_set_to_0.2", "r"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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304 ) as expected:
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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305 expected_content = expected.read()
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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306
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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307 with open(output_file, "r") as out_file:
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308 output_content = out_file.read()
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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309
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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310 assert expected_content == output_content
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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311
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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312 def test_12_YIL115C_Anc_2_253_codon_aln(self):
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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313 """
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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314 test kpi_gappy with codon alignment of yeast sequences
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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315 usage: clipkit 12_YIL115C_Anc_2.253_codon_aln.fasta -g 0.3 -m kpi-gappy
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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316 """
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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317 input_file = f"{here.parent}/samples/12_YIL115C_Anc_2.253_codon_aln.fasta"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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318 output_file = "output/12_YIL115C_Anc_2.253_codon_aln.fasta.clipkit"
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319
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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320 kwargs = dict(
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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321 input_file=input_file,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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322 output_file=output_file,
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323 input_file_format='fasta',
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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324 output_file_format='fasta',
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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325 complement=False,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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326 gaps=0.3,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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327 mode=TrimmingMode.kpi_gappy,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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328 use_log=False,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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329 )
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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330 execute(**kwargs)
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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331
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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332 with open(
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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333 f"{here.parent}/expected/12_YIL115C_Anc_2.253_codon_aln.fasta_kpi_gappy_custom_gaps",
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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334 "r",
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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335 ) as expected:
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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336 expected_content = expected.read()
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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337
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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338 with open(output_file, "r") as out_file:
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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339 output_content = out_file.read()
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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340
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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341 assert expected_content == output_content
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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342
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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343 def test_24_ENSG00000163519_codon_aln(self):
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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344 """
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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345 test kpi_gappy with codon alignment of mammalian sequences
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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346 usage: clipkit 24_ENSG00000163519_codon_aln.fasta -g .4 -m kpi-gappy
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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diff changeset
347 """
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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348 input_file = f"{here.parent}/samples/24_ENSG00000163519_codon_aln.fasta"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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349 output_file = "output/24_ENSG00000163519_codon_aln.fasta.clipkit"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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350
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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351 kwargs = dict(
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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352 input_file=input_file,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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353 output_file=output_file,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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354 input_file_format='fasta',
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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355 output_file_format='fasta',
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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356 complement=False,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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diff changeset
357 gaps=0.4,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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358 mode=TrimmingMode.kpi_gappy,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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359 use_log=False,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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360 )
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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361 execute(**kwargs)
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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diff changeset
362
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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diff changeset
363 with open(
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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364 f"{here.parent}/expected/24_ENSG00000163519_codon_aln.fasta_kpi_gappy_custom_gaps",
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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365 "r",
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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366 ) as expected:
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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367 expected_content = expected.read()
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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diff changeset
368
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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369 with open(output_file, "r") as out_file:
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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370 output_content = out_file.read()
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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diff changeset
371
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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diff changeset
372 assert expected_content == output_content
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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diff changeset
373
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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374 def test_EOG091N44M8_nt(self):
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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diff changeset
375 """
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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376 test kpi_gappy with nucleotide alignment of Penicillium sequences
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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377 usage: clipkit EOG091N44M8_nt.fa -g .1 -m kpi-gappy
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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diff changeset
378 """
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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diff changeset
379 input_file = f"{here.parent}/samples/EOG091N44M8_nt.fa"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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diff changeset
380 output_file = "output/EOG091N44M8_nt.fa.clipkit"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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diff changeset
381
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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diff changeset
382 kwargs = dict(
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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diff changeset
383 input_file=input_file,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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diff changeset
384 output_file=output_file,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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diff changeset
385 input_file_format='fasta',
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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386 output_file_format='fasta',
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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387 complement=False,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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diff changeset
388 gaps=0.1,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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diff changeset
389 mode=TrimmingMode.kpi_gappy,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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diff changeset
390 use_log=False,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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diff changeset
391 )
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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diff changeset
392 execute(**kwargs)
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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diff changeset
393
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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diff changeset
394 with open(
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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diff changeset
395 f"{here.parent}/expected/EOG091N44M8_nt.fa_kpi_gappy_custom_gaps", "r"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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396 ) as expected:
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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397 expected_content = expected.read()
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398
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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399 with open(output_file, "r") as out_file:
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400 output_content = out_file.read()
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401
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402 assert expected_content == output_content
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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403
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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404 @pytest.mark.slow
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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405 def test_EOG092C0CZK_aa(self):
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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406 """
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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407 test kpi_gappy with amino alignment of fungal sequences
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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408 usage: clipkit EOG092C0CZK_aa_aln.fasta -g .5 -m kpi-gappy
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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409 """
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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410 input_file = f"{here.parent}/samples/EOG092C0CZK_aa_aln.fasta"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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411 output_file = "output/EOG092C0CZK_aa_aln.fasta.clipkit"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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412
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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413 kwargs = dict(
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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414 input_file=input_file,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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415 output_file=output_file,
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416 input_file_format='fasta',
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417 output_file_format='fasta',
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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418 complement=False,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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419 gaps=0.5,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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420 mode=TrimmingMode.kpi_gappy,
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421 use_log=False,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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422 )
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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423 execute(**kwargs)
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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424
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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425 with open(
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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426 f"{here.parent}/expected/EOG092C0CZK_aa_aln.fasta_kpi_gappy_custom_gaps",
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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427 "r",
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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428 ) as expected:
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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429 expected_content = expected.read()
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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430
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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431 with open(output_file, "r") as out_file:
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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432 output_content = out_file.read()
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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433
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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434 assert expected_content == output_content
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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435
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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436 @pytest.mark.slow
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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437 def test_EOG092C4VOX_aa(self):
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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438 """
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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439 test kpi_gappy with amino alignment of fungal sequences
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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440 usage: clipkit EOG092C4VOX_aa_aln.fasta -g .25 -m kpi-gappy
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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441 """
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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442 input_file = f"{here.parent}/samples/EOG092C4VOX_aa_aln.fasta"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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443 output_file = "output/EOG092C4VOX_aa_aln.fasta.clipkit"
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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444
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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445 kwargs = dict(
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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446 input_file=input_file,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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447 output_file=output_file,
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448 input_file_format='fasta',
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449 output_file_format='fasta',
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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450 complement=False,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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451 gaps=0.25,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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452 mode=TrimmingMode.kpi_gappy,
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453 use_log=False,
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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454 )
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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455 execute(**kwargs)
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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456
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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457 with open(
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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458 f"{here.parent}/expected/EOG092C4VOX_aa_aln.fasta_kpi_gappy_custom_gaps",
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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459 "r",
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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460 ) as expected:
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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461 expected_content = expected.read()
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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462
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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463 with open(output_file, "r") as out_file:
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464 output_content = out_file.read()
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465
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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466 assert expected_content == output_content