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annotate clipkit_repo/tests/integration/test_smart_gap_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
49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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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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7
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8 here = Path(__file__)
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9
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10
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11 @pytest.mark.integration
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12 class TestSmartGapsMode(object):
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13 def test_simple_no_change(self):
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14 """
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15 usage: clipkit simple.fa
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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/simple.fa_smart_gaps"
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19 kwargs = dict(
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20 input_file=input_file,
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21 output_file=output_file,
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22 input_file_format='fasta',
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23 output_file_format='fasta',
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24 complement=False,
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25 gaps=0.8,
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26 mode=TrimmingMode.smart_gap,
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27 use_log=False,
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28 )
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29 execute(**kwargs)
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30
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31 with open(
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32 f"{here.parent}/expected/simple.fa_smart_gaps", "r"
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33 ) as expected:
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34 expected_content = expected.read()
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35
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36 with open(output_file, "r") as out_file:
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37 output_content = out_file.read()
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38
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39 assert expected_content == output_content
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40
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41 def test_simple_simple_long_description_no_change(self):
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42 """
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43 usage: clipkit simple_long_description.fa
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44 """
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45 input_file = f"{here.parent}/samples/simple_long_description.fa"
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46 output_file = "output/simple_long_description.fa_smart_gaps"
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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=0.8,
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54 mode=TrimmingMode.smart_gap,
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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(
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60 f"{here.parent}/expected/simple_long_description.fa_smart_gaps", "r"
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61 ) as expected:
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62 expected_content = expected.read()
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63
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64 with open(output_file, "r") as out_file:
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65 output_content = out_file.read()
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66
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67 assert expected_content == output_content
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68
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69 def test_12_YIL115C_Anc_2_253_codon_aln(self):
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70 """
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71 test gappy with codon alignment of yeast sequences
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72 usage: clipkit 12_YIL115C_Anc_2.253_codon_aln.fasta
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73 """
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74 input_file = f"{here.parent}/samples/12_YIL115C_Anc_2.253_codon_aln.fasta"
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75 output_file = "output/12_YIL115C_Anc_2.253_codon_aln.fasta.clipkit_smart_gaps"
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76 in_file_format = 'fasta'
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77 out_file_format = 'fasta'
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78
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79 kwargs = dict(
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80 input_file=input_file,
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81 output_file=output_file,
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82 input_file_format='fasta',
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83 output_file_format='fasta',
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84 complement=False,
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85 gaps=0.9167,
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86 mode=TrimmingMode.smart_gap,
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87 use_log=False,
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88 )
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89 execute(**kwargs)
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90
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91 with open(
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92 f"{here.parent}/expected/12_YIL115C_Anc_2.253_codon_aln.clipkit_smart_gaps", "r"
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93 ) as expected:
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94 expected_content = expected.read()
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95
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96 with open(output_file, "r") as out_file:
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97 output_content = out_file.read()
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98
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99 assert expected_content == output_content
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100
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101 def test_12_YIL115C_Anc_2_253_aa_aln(self):
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102 """
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103 test gappy with amino acid alignment of yeast sequences
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104 usage: clipkit 12_YIL115C_Anc_2.253_aa_aln.fasta
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105 """
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106 input_file = f"{here.parent}/samples/12_YIL115C_Anc_2.253_aa_aln.fasta"
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107 output_file = "output/12_YIL115C_Anc_2.253_aa_aln.fasta.clipkit_smart_gaps"
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108 in_file_format = 'fasta'
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109 out_file_format = 'fasta'
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110
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111 kwargs = dict(
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112 input_file=input_file,
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113 output_file=output_file,
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114 input_file_format='fasta',
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115 output_file_format='fasta',
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116 complement=False,
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117 gaps=0.9167,
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118 mode=TrimmingMode.smart_gap,
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119 use_log=False,
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120 )
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121 execute(**kwargs)
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122
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123 with open(
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124 f"{here.parent}/expected/12_YIL115C_Anc_2.253_aa_aln.clipkit_smart_gaps", "r"
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125 ) as expected:
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126 expected_content = expected.read()
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127
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128 with open(output_file, "r") as out_file:
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129 output_content = out_file.read()
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130
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131 assert expected_content == output_content
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132
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133 def test_24_ENSG00000163519_aa_aln(self):
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134 """
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135 test gappy with amino acid alignment of mammalian sequences
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136 usage: clipkit 24_ENSG00000163519_aa_aln.fasta
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137 """
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138 input_file = f"{here.parent}/samples/24_ENSG00000163519_aa_aln.fasta"
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139 output_file = "output/24_ENSG00000163519_aa_aln.fasta.clipkit"
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140 in_file_format = 'fasta'
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141 out_file_format = 'fasta'
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142
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143 kwargs = dict(
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144 input_file=input_file,
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145 output_file=output_file,
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146 input_file_format='fasta',
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147 output_file_format='fasta',
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148 complement=False,
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149 gaps=0.9583,
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150 mode=TrimmingMode.smart_gap,
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151 use_log=False,
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152 )
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153 execute(**kwargs)
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154
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155 with open(
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156 f"{here.parent}/expected/24_ENSG00000163519_aa_aln.clipkit_smart_gaps", "r"
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157 ) as expected:
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158 expected_content = expected.read()
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159
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160 with open(output_file, "r") as out_file:
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161 output_content = out_file.read()
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162
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163 assert expected_content == output_content
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164
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165 def test_24_ENSG00000163519_codon_aln(self):
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166 """
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167 test gappy with codon alignment of mammalian sequences
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168 usage: clipkit 24_ENSG00000163519_codon_aln.fasta
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169 """
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170 input_file = f"{here.parent}/samples/24_ENSG00000163519_codon_aln.fasta"
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171 output_file = "output/24_ENSG00000163519_codon_aln.fasta.clipkit"
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172 in_file_format = 'fasta'
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173 out_file_format = 'fasta'
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174
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175 kwargs = dict(
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176 input_file=input_file,
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177 output_file=output_file,
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178 input_file_format='fasta',
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179 output_file_format='fasta',
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180 complement=False,
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181 gaps=0.9583,
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182 mode=TrimmingMode.smart_gap,
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183 use_log=False,
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184 )
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185 execute(**kwargs)
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186
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187 with open(
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188 f"{here.parent}/expected/24_ENSG00000163519_codon_aln.clipkit_smart_gaps", "r"
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189 ) as expected:
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190 expected_content = expected.read()
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191
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192 with open(output_file, "r") as out_file:
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193 output_content = out_file.read()
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194
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195 assert expected_content == output_content
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196
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197 def test_EOG091N44M8_aa(self):
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198 """
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199 test gappy with amino acid alignment of Penicillium sequences
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200 usage: clipkit EOG091N44M8_aa.fa
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201 """
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202 input_file = f"{here.parent}/samples/EOG091N44M8_aa.fa"
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203 output_file = "output/EOG091N44M8_aa.fa.clipkit"
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204 in_file_format = 'fasta'
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205 out_file_format = 'fasta'
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206
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207 kwargs = dict(
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208 input_file=input_file,
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209 output_file=output_file,
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210 input_file_format='fasta',
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211 output_file_format='fasta',
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212 complement=False,
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213 gaps=0.8803,
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214 mode=TrimmingMode.smart_gap,
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215 use_log=False,
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216 )
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217 execute(**kwargs)
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218
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219 with open(f"{here.parent}/expected/EOG091N44M8_aa.clipkit_smart_gaps", "r") as expected:
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220 expected_content = expected.read()
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221
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222 with open(output_file, "r") as out_file:
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223 output_content = out_file.read()
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224
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225 assert expected_content == output_content
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226
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227 def test_EOG091N44M8_nt(self):
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228 """
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229 test gappy with nucleotide alignment of Penicillium sequences
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230 usage: clipkit EOG091N44M8_nt.fa
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231 """
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232 input_file = f"{here.parent}/samples/EOG091N44M8_nt.fa"
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233 output_file = "output/EOG091N44M8_nt.fa.clipkit"
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234 in_file_format = 'fasta'
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235 out_file_format = 'fasta'
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236
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237 kwargs = dict(
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238 input_file=input_file,
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239 output_file=output_file,
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240 input_file_format='fasta',
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241 output_file_format='fasta',
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242 complement=False,
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243 gaps=0.8803,
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244 mode=TrimmingMode.smart_gap,
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245 use_log=False,
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246 )
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247 execute(**kwargs)
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248
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249 with open(f"{here.parent}/expected/EOG091N44M8_nt.clipkit_smart_gaps", "r") as expected:
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250 expected_content = expected.read()
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251
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252 with open(output_file, "r") as out_file:
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253 output_content = out_file.read()
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254
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255 assert expected_content == output_content
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256
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257 @pytest.mark.slow
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258 def test_EOG092C4VOX_aa(self):
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259 """
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260 test gappy with amino alignment of fungal sequences
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261 usage: clipkit EOG092C4VOX_aa_aln.fasta
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262 """
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263 input_file = f"{here.parent}/samples/EOG092C4VOX_aa_aln.fasta"
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264 output_file = "output/EOG092C4VOX_aa_aln.fasta.clipkit"
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265 in_file_format = 'fasta'
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266 out_file_format = 'fasta'
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267
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268 kwargs = dict(
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269 input_file=input_file,
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270 output_file=output_file,
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271 input_file_format='fasta',
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272 output_file_format='fasta',
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273 complement=False,
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274 gaps=0.9993,
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275 mode=TrimmingMode.smart_gap,
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276 use_log=False,
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277 )
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278 execute(**kwargs)
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279
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280 with open(
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281 f"{here.parent}/expected/EOG092C4VOX_aa_aln.clipkit_smart_gaps", "r"
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282 ) as expected:
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283 expected_content = expected.read()
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284
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285 with open(output_file, "r") as out_file:
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286 output_content = out_file.read()
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287
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288 assert expected_content == output_content