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annotate clipkit_repo/tests/integration/test_complementary_output.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 TestComplementOut(object):
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13 def test_simple_complement(self):
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14 """
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15 test complementary output file with a simple case
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16 usage: clipkit simple.fa -c
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17 """
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18 output_file = "output/simple.fa_gappy"
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19 complement_out_file = f"{output_file}.complement"
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20
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21 kwargs = dict(
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22 input_file=f"{here.parent}/samples/simple.fa",
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23 output_file=output_file,
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24 input_file_format='fasta',
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25 output_file_format='fasta',
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26 complement=True,
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27 gaps=0.9,
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28 mode=TrimmingMode.gappy,
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29 use_log=False,
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30 )
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31
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32 execute(**kwargs)
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33
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34 with open(
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35 f"{here.parent}/expected/simple.fa_gappy.complement", "r"
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36 ) as expected:
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37 expected_content = expected.read()
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38
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39 with open(complement_out_file, "r") as out_file:
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40 output_content = out_file.read()
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41
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42 assert expected_content == output_content
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43
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44 def test_simple_long_description_complement(self):
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45 """
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46 test complementary output file with a simple case
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47 usage: clipkit simple_long_description.fa -c
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48 """
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49 output_file = "output/simple_long_description.fa_gappy"
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50 complement_out_file = f"{output_file}.complement"
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51
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52 kwargs = dict(
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53 input_file=f"{here.parent}/samples/simple_long_description.fa",
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54 output_file=output_file,
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55 input_file_format='fasta',
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56 output_file_format='fasta',
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57 complement=True,
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58 gaps=0.9,
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59 mode=TrimmingMode.gappy,
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60 use_log=False,
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61 )
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62
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63 execute(**kwargs)
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64
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65 with open(
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66 f"{here.parent}/expected/simple_long_description.fa_gappy.complement", "r"
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67 ) as expected:
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68 expected_content = expected.read()
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69
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70 with open(complement_out_file, "r") as out_file:
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71 output_content = out_file.read()
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72
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73 assert expected_content == output_content
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74
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75 def test_12_YIL115C_Anc_2_253_aa_aln_complement(self):
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76 """
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77 test complementary output file for amino acid yeast sequences
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78 usage: clipkit 12_YIL115C_Anc_2.253_aa_aln.fasta -c
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79 """
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80 output_file = "output/12_YIL115C_Anc_2.253_aa_aln.fasta_gappy"
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81 complement_out_file = f"{output_file}.complement"
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82
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83 kwargs = dict(
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84 input_file=f"{here.parent}/samples/12_YIL115C_Anc_2.253_aa_aln.fasta",
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85 output_file=output_file,
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86 input_file_format='fasta',
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87 output_file_format='fasta',
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88 complement=True,
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89 gaps=0.9,
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90 mode=TrimmingMode.gappy,
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91 use_log=False,
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92 )
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93 execute(**kwargs)
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94
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95 with open(
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96 f"{here.parent}/expected/12_YIL115C_Anc_2.253_aa_aln.fasta_gappy.complement",
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97 "r",
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98 ) as expected:
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99 expected_content = expected.read()
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100
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101 with open(complement_out_file, "r") as out_file:
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102 output_content = out_file.read()
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103
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104 assert expected_content == output_content
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105
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106 def test_EOG091N44M8_aa_complement(self):
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107 """
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108 test complementary output file for amino acid Penicillium sequences
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109 usage: clipkit EOG091N44M8_aa.fa -c
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110 """
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111 output_file = "output/EOG091N44M8_aa.fa_gappy"
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112 complement_out_file = f"{output_file}.complement"
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113
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114 kwargs = dict(
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115 input_file=f"{here.parent}/samples/EOG091N44M8_aa.fa",
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116 output_file=output_file,
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117 input_file_format='fasta',
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118 output_file_format='fasta',
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119 complement=True,
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120 gaps=0.9,
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121 mode=TrimmingMode.gappy,
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122 use_log=False,
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123 )
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124 execute(**kwargs)
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125
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126 with open(
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127 f"{here.parent}/expected/EOG091N44M8_aa.fa_gappy.complement", "r"
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128 ) as expected:
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129 expected_content = expected.read()
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130
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131 with open(complement_out_file, "r") as out_file:
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132 output_content = out_file.read()
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133
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134 assert expected_content == output_content