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1 #!/usr/bin/env python3
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2 '''
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3 Basic Tarean and RepeatExplorer tests
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4 '''
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5 import subprocess
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6 import tempfile
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7 import unittest
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8 import os
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9 import shutil
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10
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11 def check_for_missing_files(directory, file_list):
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12 ''' check if files exists in the directory '''
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13 missing_files = []
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14 for f in file_list:
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15 path = os.path.join(directory, f)
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16 if os.path.exists(path):
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17 continue
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18 else:
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19 missing_files.append(f)
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20 return missing_files
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21
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22
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23 class TestBasic(unittest.TestCase):
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24 ''' basic repex-tarean testcase '''
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25 EXECUTABLE = "./seqclust"
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26
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27 # file lists to check
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28 FILE_LIST_BASIC = [
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29 "./seqclust/clustering/clusters/dir_CL0001/hitsort_part.csv",
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30 "./seqclust/clustering/clusters/dir_CL0001/reads.fasta",
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31 "./seqclust/clustering/clusters/dir_CL0001/reads_selection.fasta",
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32 "./seqclust/clustering/clusters/dir_CL0001/dna_database_annotation.csv",
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33 "./seqclust/clustering/clusters/dir_CL0001/graph_layout.GL",
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34 "./seqclust/clustering/clusters/dir_CL0001/graph_layout.png",
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35 "./seqclust/clustering/clusters/dir_CL0001/graph_layout_tmb.png",
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36 "./seqclust/clustering/clusters/dir_CL0001/graph_layout_directed.RData",
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37 "./logfile.txt", "./style1.css", "./documentation.html",
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38 "./tarean_report.html", "./cluster_report.html",
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39 "./summary_histogram.png", "./index.html", "./sequences.db",
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40 "./hitsort.db", "./TAREAN_consensus_rank_1.fasta",
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41 "./TAREAN_consensus_rank_2.fasta", "./TAREAN_consensus_rank_3.fasta",
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42 "./TAREAN_consensus_rank_4.fasta", "./seqclust/clustering/hitsort",
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43 "./seqclust/clustering/hitsort.cls"
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44 ]
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45 FILE_LIST_ASSEMBLY = [
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46 "./seqclust/small_clusters_assembly/small_clusters.aln",
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47 "./seqclust/small_clusters_assembly/small_clusters.ace",
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48 "./seqclust/small_clusters_assembly/small_clusters.fasta"
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49 ]
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50 FILE_LIST_FILTERING = ["./seqclust/prerun/filter_sequences.fasta"]
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51 FILE_LIST_COMPARATIVE = ["COMPARATIVE_ANALYSIS_COUNTS.csv"]
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52 FILE_LIST_CUSTOM_DATABASE = [
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53 "./seqclust/custom_databases/extra_database",
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54 "./seqclust/clustering/clusters/dir_CL0001/custom_db_extra_database_annotation.csv"
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55 ]
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56 def setUp(self):
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57 pass
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58
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59 # helper function
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60 def tarean_run(self, cmd_options, file_list):
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61 ''' Basic taren run '''
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62 # output goes to tmp directory
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63 tmpdir = tempfile.mkdtemp()
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64 logfile = tempfile.NamedTemporaryFile(delete=False)
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65 print("\n------------------------------------------------------")
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66 print("Temp files:")
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67 print(" tmpdir : ", tmpdir)
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68 print(" logfile : ", logfile.name)
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69 print("------------------------------------------------------")
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70 print([self.EXECUTABLE] + ['-l', logfile.name, '-v', tmpdir] + cmd_options)
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71 p = subprocess.Popen(
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72 args=[self.EXECUTABLE] + ['-l', logfile.name, '-v', tmpdir
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73 ] + cmd_options)
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74 p.wait()
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75 status = p.returncode
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76 missing_files = check_for_missing_files(directory=tmpdir,
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77 file_list=file_list)
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78 if status:
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79 # print log file
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80 print("Non zero exit status!")
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81 with open(logfile.name) as f:
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82 print(f.read())
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83
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84 self.assertEqual(status, 0)
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85 self.assertEqual(
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86 len(missing_files),
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87 0,
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88 msg="\n missing files: \n" + "\n".join(missing_files))
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89 shutil.rmtree(tmpdir)
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90 os.remove(logfile.name)
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91
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92
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93 def test_help(self):
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94 '''Test if help option works '''
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95 p = subprocess.Popen(args=[self.EXECUTABLE, "-h"],
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96 stdout=subprocess.PIPE)
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97 output = str(p.stdout.readlines())
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98 p.stdout.close()
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99 p.wait()
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100 status = p.returncode
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101 self.assertRegex(output, "usage")
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102 self.assertRegex(output, "optional arguments")
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103 self.assertEqual(status, 0)
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104
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105 def test_basic_no_merging_tarean(self):
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106 ''' Basic taren run '''
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107 cmd_options = ['-t', '-p', '-s', '6000', 'test_data/LAS_paired_10k.fas']
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108 self.tarean_run(cmd_options, file_list=self.FILE_LIST_BASIC)
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109
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110 def test_basic_with_merging_tarean(self):
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111 ''' Basic taren run '''
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112 cmd_options = ['-t', '-p', '-M', '0.2', '-s', '6000',
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113 'test_data/LAS_paired_10k.fas']
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114 self.tarean_run(cmd_options, file_list=self.FILE_LIST_BASIC)
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115
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116
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117 def test_basic_with_merging_tarean_dust_off(self):
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118 ''' Basic taren run '''
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119 cmd_options = ['-t', '-p', '-M', '0.2', '-s', '6000', "-opt", "ILLUMINA_DUST_OFF",
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120 'test_data/LAS_paired_10k.fas']
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121 self.tarean_run(cmd_options, file_list=self.FILE_LIST_BASIC)
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122
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123 def test_long_with_merging_tarean(self):
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124 '''Using more data with tarean'''
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125 cmd_options = ['-t', '-p', '-M', '0.1', '-m', '0.01',
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126 'test_data/LAS_paired_25k.fas']
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127 self.tarean_run(cmd_options, file_list=self.FILE_LIST_BASIC)
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128
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129 def test_long_with_merging2_tarean(self):
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130 '''Using more data with tarean 300k reads'''
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131 cmd_options = ['-t', '-p', '-M', '0.1', '-m', '0.01',
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132 'test_data/LAS_paired_300k.fas']
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133 self.tarean_run(cmd_options, file_list=self.FILE_LIST_BASIC)
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134
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135 def test_short_comparative_re(self):
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136 '''comparative analysis, two species, small run'''
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137 cmd_options = ['-P','3', '-p', '-m', '0.01',
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138 'test_data/sequences_comparative.fasta']
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139 self.tarean_run(cmd_options, file_list=self.FILE_LIST_BASIC + self.FILE_LIST_COMPARATIVE)
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140
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141 # REPEATEXPLORER - full runs
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142 def test_basic_no_merging_re(self):
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143 ''' Basic taren run '''
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144 cmd_options = ['-p', '-s', '6000', 'test_data/LAS_paired_10k.fas']
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145 self.tarean_run(cmd_options, file_list=self.FILE_LIST_BASIC + self.FILE_LIST_ASSEMBLY)
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146
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147 def test_basic_no_merging_re_diamond(self):
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148 ''' Basic taren run '''
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149 cmd_options = ['-p', '-s', '6000','-D','DIAMOND', 'test_data/LAS_paired_10k.fas']
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150 self.tarean_run(cmd_options, file_list=self.FILE_LIST_BASIC + self.FILE_LIST_ASSEMBLY)
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151
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152
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153
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154 def test_basic_with_merging_re(self):
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155 ''' Basic taren run '''
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156 cmd_options = ['-p', '-M', '0.2', '-s', '6000',
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157 'test_data/LAS_paired_10k.fas']
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158 self.tarean_run(cmd_options, file_list=self.FILE_LIST_BASIC + self.FILE_LIST_ASSEMBLY)
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159
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160 def test_long_with_merging_re(self):
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161 '''Using more data with tarean'''
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162 cmd_options = ['-p', '-M', '0.1', '-m', '0.01',
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163 'test_data/LAS_paired_25k.fas']
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164 self.tarean_run(cmd_options, file_list=self.FILE_LIST_BASIC + self.FILE_LIST_ASSEMBLY)
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165
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166 def test_long_with_merging_re_diamond(self):
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167 '''Using more data with tarean and using diamond'''
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168 cmd_options = ['-p', '-M', '0.1', '-m', '0.01','-D','DIAMOND',
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169 'test_data/LAS_paired_25k.fas']
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170 self.tarean_run(cmd_options, file_list=self.FILE_LIST_BASIC + self.FILE_LIST_ASSEMBLY)
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171
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172 def test_long_with_merging2_re(self):
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173 '''Using more data with tarean 300k reads'''
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174 cmd_options = ['-p', '-M', '0.1', '-m', '0.01',
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175 'test_data/LAS_paired_300k.fas']
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176 self.tarean_run(cmd_options, file_list=self.FILE_LIST_BASIC + self.FILE_LIST_ASSEMBLY)
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177
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178 def test_long_with_merging_and_filtering_re(self):
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179 '''Using more data with tarean, test of automatic filtering'''
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180 cmd_options = ['-A', '-p', '-M', '0.2', '-m', '0.01',
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181 'test_data/ceu_200k.fasta']
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182 self.tarean_run(
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183 cmd_options,
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184 file_list=self.FILE_LIST_BASIC + self.FILE_LIST_FILTERING + self.FILE_LIST_ASSEMBLY)
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185
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186 def test_custom_database_re(self):
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187 ''' Basic taren run '''
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188 cmd_options = ['-p', '-d', 'test_data/extra_database', 'extra_database', 'test_data/LAS_paired_10k.fas']
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189 self.tarean_run(cmd_options, file_list=self.FILE_LIST_BASIC + self.FILE_LIST_CUSTOM_DATABASE)
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190
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191 def tearDown(self):
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192 pass
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193
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194
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195 SHORT_TASK_NAME_LIST_TAREAN = ['test_help', 'test_basic_no_merging_tarean',
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196 'test_basic_with_merging_tarean',
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197 'test_basic_with_merging_tarean_dust_off']
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198 LONG_TASK_NAME_LIST_TAREAN = ['test_long_with_merging_tarean',
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199 'test_long_with_merging2_tarean']
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200 SHORT_TASK_NAME_LIST_RE = ['test_basic_no_merging_re',
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201 'test_basic_with_merging_re',
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202 'test_basic_no_merging_re_diamond']
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203 LONG_TASK_NAME_LIST_RE = ['test_long_with_merging_re',
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204 'test_long_with_merging2_re',
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205 'test_long_with_merging_and_filtering_re',
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206 'test_long_with_merging_re_diamond']
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207
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208 COMPARATIVE_LIST = ['test_short_comparative_re']
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209 CUSTOM_DATABASE_LIST = ['test_short_custom_database']
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210
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211 # Test suites:
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212 SHORT_TAREAN_SUITE = unittest.TestSuite([TestBasic(i)
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213 for i in SHORT_TASK_NAME_LIST_TAREAN])
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214 LONG_TAREAN_SUITE = unittest.TestSuite([TestBasic(i)
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215 for i in LONG_TASK_NAME_LIST_TAREAN])
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216 COMPARATIVE_SUITE = unittest.TestSuite([TestBasic(i) for i in COMPARATIVE_LIST])
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217 CUSTOM_DB_SUITE = unittest.TestSuite([TestBasic('test_custom_database_re')])
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218
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219 SHORT_RE_SUITE = unittest.TestSuite([TestBasic(i) for i in SHORT_TASK_NAME_LIST_RE])
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220 LONG_RE_SUITE = unittest.TestSuite([TestBasic(i) for i in LONG_TASK_NAME_LIST_RE])
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221
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222 SHORT_SUITE = unittest.TestSuite([SHORT_RE_SUITE, SHORT_TAREAN_SUITE,
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223 COMPARATIVE_SUITE, CUSTOM_DB_SUITE])
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224
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225 LONG_LONG = unittest.TestSuite([LONG_RE_SUITE, LONG_TAREAN_SUITE])
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226
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227 # for single test tesing
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228 if __name__ == '__main__':
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229 unittest.main(verbosity=2)
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