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1 import subprocess
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2 import unittest
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3 import os
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4 from commons.core.utils.FileUtils import FileUtils
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5 from commons.core.sql.DbMySql import DbMySql
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6 from commons.tools.GetMultAlignAndPhylogenyPerTErefSeq import GetMultAlignAndPhylogenyPerTErefSeq
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7 from shutil import rmtree
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8 from glob import glob
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9
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10 class Test_F_GetMultAlignAndPhylogenyPerTErefSeq(unittest.TestCase):
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11
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12 def setUp(self):
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13 self._verbosity = 3
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14
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15 self._testPrefix = 'Test_GMAAPperTErefSeq_'
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16 self._configFileName = "%sConfig.cfg" % self._testPrefix
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17 self._iDb = DbMySql()
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18
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19 self.inPathTableName = "%sDmelChr4_chr_allTEs_nr_noSSR_join_path" % (self._testPrefix)
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20 self.inPathFileName = "%s/Tools/DmelChr4_chr_allTEs_nr_noSSR_join_path.path" % os.environ["REPET_DATA"]
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21 self._iDb.createTable(self.inPathTableName, "path", self.inPathFileName, True)
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22
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23 self.RefTETableName = "%sDmelChr4_refTEs" % (self._testPrefix)
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24 self.RefTEFileName = "%s/Tools/DmelChr4_refTEs.fa" % os.environ["REPET_DATA"]
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25 self._iDb.createTable(self.RefTETableName, "seq", self.RefTEFileName, True)
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26
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27 self.genomeTableName = "%sDmelChr4_chr" % (self._testPrefix)
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28 self.genomeFileName = "%s/Tools/DmelChr4.fa" % os.environ["REPET_DATA"]
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29 self._iDb.createTable(self.genomeTableName, "seq", self.genomeFileName, True)
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30
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31 try:
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32 os.makedirs(self._testPrefix)
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33 except:pass
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34 os.chdir(self._testPrefix)
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35 self._writeConfigFile()
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36
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37 # self._expFileName_FullLengthCopy = "%s/Tools/GiveInfoTeAnnotFile_ConsensusWithFullLengthCopy.txt" % os.environ["REPET_DATA"]
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38 # self._expFileName_Copy = "%s/Tools/GiveInfoTeAnnotFile_ConsensusWithCopy.txt" % os.environ["REPET_DATA"]
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39 # self._expFileName_FullLengthFrag = "%s/Tools/GiveInfoTeAnnotFile_ConsensusWithFullLengthFrag.txt" % os.environ["REPET_DATA"]
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40 # self._expFastaFileName_FullLengthCopy = "%s/Tools/GiveInfoTeAnnotFile_ConsensusWithFullLengthCopy.fa" % os.environ["REPET_DATA"]
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41 # self._expFastaFileName_Copy = "%s/Tools/GiveInfoTeAnnotFile_ConsensusWithCopy.fa" % os.environ["REPET_DATA"]
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42 # self._expFastaFileName_FullLengthFrag = "%s/Tools/GiveInfoTeAnnotFile_ConsensusWithFullLengthFrag.fa" % os.environ["REPET_DATA"]
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43
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44
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45 # inputFastaFileName = "input_TEannot_refTEs.fa"
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46 # os.symlink(self._expFastaFileName_Copy, inputFastaFileName)
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47
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48 # self._tableName = "Dummy_Atha_refTEs_seq"
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49 # self._iDb.createTable(self._tableName, "seq", inputFastaFileName, True)
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50 # os.remove(inputFastaFileName)
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51 #
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52 # self._obsFileName_FullLengthCopy = "%s_FullLengthCopy.txt" % os.path.splitext(os.path.basename(self._inFileName))[0]
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53 # self._obsFileName_Copy = "%s_OneCopyAndMore.txt" % os.path.splitext(os.path.basename(self._inFileName))[0]
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54 # self._obsFileName_FullLengthFrag = "%s_FullLengthFrag.txt" % os.path.splitext(os.path.basename(self._inFileName))[0]
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55 # self._obsFastaFileName_FullLengthCopy = "%s.fa" % os.path.splitext(self._obsFileName_FullLengthCopy)[0]
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56 # self._obsFastaFileName_Copy = "%s.fa" % os.path.splitext(self._obsFileName_Copy)[0]
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57 # self._obsFastaFileName_FullLengthFrag = "%s.fa" % os.path.splitext(self._obsFileName_FullLengthFrag)[0]
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58
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59 def tearDown(self):
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60 # self._iDb.dropTable(self.inPathTableName)
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61 # self._iDb.dropTable(self.RefTETableName)
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62 # self._iDb.dropTable(self.genomeTableName)
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63 # self._iDb.close()
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64
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65 os.chdir("..")
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66 # try:
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67 # rmtree(self._testPrefix)
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68 # except:pass
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69
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70
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71 # def test_run_step1(self):
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72 # iGMAAPperTErefSeq = GetMultAlignAndPhylogenyPerTErefSeq(pathTableName= self.inPathTableName, refSeqTableName=self.RefTETableName, genomeSeqTableName= self.genomeTableName, configFileName=self._configFileName, step=1, verbosity=self._verbosity)
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73 # iGMAAPperTErefSeq.run()
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74 #
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75 # copiesFiles = glob("*_copies.fa")
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76 # self.assertTrue(len(copiesFiles) > 0)
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77 # self.assertTrue(os.stat("DmelChr4-B-R9-Map3_NoCat_copies.fa")[6] != 0)#check if file is empty
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78 #
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79 # def test_run_step1Step2Map(self):
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80 # iGMAAPperTErefSeq = GetMultAlignAndPhylogenyPerTErefSeq(pathTableName= self.inPathTableName, refSeqTableName=self.RefTETableName, genomeSeqTableName= self.genomeTableName, mSAmethod="Map", configFileName=self._configFileName, step=1, verbosity=self._verbosity)
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81 # iGMAAPperTErefSeq.run()
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82 # iGMAAPperTErefSeq.step = 2
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83 # iGMAAPperTErefSeq.run()
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84 #
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85 # self.assertTrue(os.stat("DmelChr4-B-G9-Map3_NoCat_all.fa.oriented_map.fa_aln")[6] != 0)
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86 #
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87 # def test_run_step1Step2RefAlign(self):
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88 # iGMAAPperTErefSeq = GetMultAlignAndPhylogenyPerTErefSeq(pathTableName= self.inPathTableName, refSeqTableName=self.RefTETableName, genomeSeqTableName= self.genomeTableName, mSAmethod="RefAlign", configFileName=self._configFileName, step=1, verbosity=self._verbosity)
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89 # iGMAAPperTErefSeq.run()
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90 # iGMAAPperTErefSeq.step = 2
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91 # iGMAAPperTErefSeq.run()
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92 #
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93 # self.assertTrue(os.stat("DmelChr4-B-G9-Map3_NoCat_all.fa.oriented_refalign.fa_aln")[6] != 0)
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94
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95 def test_run_step1Step2Step3Map(self):
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96 iGMAAPperTErefSeq = GetMultAlignAndPhylogenyPerTErefSeq(pathTableName= self.inPathTableName, refSeqTableName=self.RefTETableName, genomeSeqTableName= self.genomeTableName, mSAmethod="Map", configFileName=self._configFileName, step=1, verbosity=self._verbosity)
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97 iGMAAPperTErefSeq.run()
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98 iGMAAPperTErefSeq.step = 2
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99 iGMAAPperTErefSeq.run()
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100 iGMAAPperTErefSeq.step = 3
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101 iGMAAPperTErefSeq.run()
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102
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103 self.assertTrue(os.stat("DmelChr4-B-G9-Map3_NoCat_all.fa.oriented_map.fa_aln")[6] != 0)
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104
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105 def _writeConfigFile(self):
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106 f = open(self._configFileName, "w")
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107 f.write("[repet_env]\n")
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108 f.write("repet_host: %s\n" % os.environ["REPET_HOST"])
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109 f.write("repet_user: %s\n" % os.environ["REPET_USER"])
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110 f.write("repet_pw: %s\n" % os.environ["REPET_PW"])
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111 f.write("repet_db: %s\n" % os.environ["REPET_DB"])
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112 f.write("repet_port: %s\n" % os.environ["REPET_PORT"])
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113 f.write("repet_job_manager: SGE\n")
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114 f.close()
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115
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116
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117 # def test_run_as_script_step1Step2Map(self):
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118 # #cmd= "GetMultAlignAndPhylogenyPerTErefSeq.py -S 1 -m 'Map' -p %s -s %s -g %s -C %s" % (self._inPathTableName,self._RefTETableName, self._genomeTableName, self._configFileName)
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119 # cmd= "GetMultAlignAndPhylogenyPerTErefSeq.py -S 1 -p %s -s %s -g %s -C %s" % (self.inPathTableName,self.RefTETableName, self.genomeTableName, self._configFileName)
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120 # subprocess.call(cmd, shell = True)
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121 #
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122 # cmd= "GetMultAlignAndPhylogenyPerTErefSeq.py -S 2 -p %s -s %s -g %s -C %s" % (self.inPathTableName,self.RefTETableName, self.genomeTableName, self._configFileName)
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123 # subprocess.call(cmd, shell = True)
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124 #
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125 # self.assertTrue(os.stat("DmelChr4-B-G9-Map3_NoCat_all.fa.oriented_map.fa_aln")[6] != 0)
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126
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127
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128 # self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName_FullLengthCopy, self._obsFileName_FullLengthCopy))
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129 # self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName_Copy, self._obsFileName_Copy))
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130 # self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName_FullLengthFrag, self._obsFileName_FullLengthFrag))
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131 # self.assertTrue(FileUtils.are2FilesIdentical(self._expFastaFileName_FullLengthCopy, self._obsFastaFileName_FullLengthCopy))
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132 # self.assertTrue(FileUtils.are2FilesIdentical(self._expFastaFileName_Copy, self._obsFastaFileName_Copy))
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133 # self.assertTrue(FileUtils.are2FilesIdentical(self._expFastaFileName_FullLengthFrag, self._obsFastaFileName_FullLengthFrag))
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134
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135 # def test_run_as_script_step2(self):
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136 # cmd= "GetMultAlignAndPhylogenyPerTErefSeq.py -S 1 -p %s -s %s -g %s -C %s" % (self._inPathTableName,self._RefTETableName, self._genomeTableName, self._configFileName)
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137 # print cmd
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138 # subprocess.call(cmd, shell = True)
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139 # self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName_FullLengthCopy, self._obsFileName_FullLengthCopy))
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140 # self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName_Copy, self._obsFileName_Copy))
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141 # self.assertTrue(FileUtils.are2FilesIdentical(self._expFileName_FullLengthFrag, self._obsFileName_FullLengthFrag))
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142 # self.assertTrue(FileUtils.are2FilesIdentical(self._expFastaFileName_FullLengthCopy, self._obsFastaFileName_FullLengthCopy))
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143 # self.assertTrue(FileUtils.are2FilesIdentical(self._expFastaFileName_Copy, self._obsFastaFileName_Copy))
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144 # self.assertTrue(FileUtils.are2FilesIdentical(self._expFastaFileName_FullLengthFrag, self._obsFastaFileName_FullLengthFrag))
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145
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146 if __name__ == "__main__":
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147 unittest.main()
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