Mercurial > repos > padge > clipkit

annotate clipkit_repo/tests/integration/test_writing_to_log_file.py @ 0:49b058e85902 draft

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"planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
author padge
date Fri, 25 Mar 2022 13:04:31 +0000
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49b058e85902 "planemo upload for repository https://github.com/jlsteenwyk/clipkit commit cbe1e8577ecb1a46709034a40dff36052e876e7a-dirty"
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1 import pytest
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2 from pathlib import Path
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4 from clipkit.clipkit import execute
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5 from clipkit.files import FileFormat
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6 from clipkit.modes import TrimmingMode
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8 here = Path(__file__)
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11 @pytest.mark.integration
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12 class TestOutLog(object):
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13 def test_simple(self):
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14 """
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15 test output in clustal format
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16 usage: clipkit simple.fa -l
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17 """
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18 input_file = f"{here.parent}/samples/simple.fa"
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19 output_file = "output/simple.fa.clipkit"
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21 kwargs = dict(
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22 input_file=input_file,
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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=False,
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27 gaps=0.9,
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28 mode=TrimmingMode.gappy,
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29 use_log=True,
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30 )
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31 execute(**kwargs)
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32
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33 with open(f"{here.parent}/expected/simple.fa.clipkit.log", "r") as expected:
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34 expected_content = expected.read()
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35
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36 with open(f"{output_file}.log", "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_long_description(self):
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42 """
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43 test output in clustal format
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44 usage: clipkit simple_long_description.fa -l
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45 """
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46 input_file = f"{here.parent}/samples/simple_long_description.fa"
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47 output_file = "output/simple_long_description.fa.clipkit"
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48
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49 kwargs = dict(
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50 input_file=input_file,
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51 output_file=output_file,
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52 input_file_format='fasta',
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53 output_file_format='fasta',
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54 complement=False,
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55 gaps=0.9,
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56 mode=TrimmingMode.gappy,
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57 use_log=True,
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58 )
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59 execute(**kwargs)
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60
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61 with open(f"{here.parent}/expected/simple_long_description.fa.clipkit.log", "r") as expected:
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62 expected_content = expected.read()
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63
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64 with open(f"{output_file}.log", "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 output in clustal format
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72 usage: clipkit 12_YIL115C_Anc_2.253_codon_aln.fasta -l
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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"
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76
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77 kwargs = dict(
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78 input_file=input_file,
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79 output_file=output_file,
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80 input_file_format='fasta',
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81 output_file_format='fasta',
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82 complement=False,
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83 gaps=0.9,
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84 mode=TrimmingMode.gappy,
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85 use_log=True,
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86 )
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87 execute(**kwargs)
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88
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89 with open(
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90 f"{here.parent}/expected/12_YIL115C_Anc_2.253_codon_aln.fasta.clipkit.log",
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91 "r",
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92 ) as expected:
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93 expected_content = expected.read()
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94
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95 with open(f"{output_file}.log", "r") as out_file:
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96 output_content = out_file.read()
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97
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98 assert expected_content == output_content
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99
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100 def test_EOG091N44M8_nt(self):
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101 """
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102 test output in clustal format
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103 usage: clipkit EOG091N44M8_nt.fa -l
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104 """
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105 input_file = f"{here.parent}/samples/EOG091N44M8_nt.fa"
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106 output_file = "output/EOG091N44M8_nt.fa.clipkit"
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107
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108 kwargs = dict(
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109 input_file=input_file,
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110 output_file=output_file,
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111 input_file_format='fasta',
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112 output_file_format='fasta',
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113 complement=False,
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114 gaps=0.9,
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115 mode=TrimmingMode.gappy,
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116 use_log=True,
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117 )
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118 execute(**kwargs)
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119
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120 with open(
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121 f"{here.parent}/expected/EOG091N44M8_nt.fa.clipkit.log", "r"
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122 ) as expected:
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123 expected_content = expected.read()
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124
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125 with open(f"{output_file}.log", "r") as out_file:
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126 output_content = out_file.read()
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127
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128 assert expected_content == output_content