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1 import os
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2 import unittest
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3 from commons.tools.TEclassifierPE import TEclassifierPE
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4 from commons.core.utils.FileUtils import FileUtils
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5 from commons.core.sql.DbFactory import DbFactory
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6
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7 class Test_F_TEclassifierPE(unittest.TestCase):
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8
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9 def test_run(self):
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10 projectName = "dummy"
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11 configFileName = "dummy.cfg"
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12 self.writeConfigFile(configFileName, projectName)
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13 inputFileName = "dummy.fa"
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14 with open(inputFileName, "w") as f:
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15 f.write(">dummySSR\n")
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16 f.write("AGTTACCATGCCCAGCATTAACCCCCCTCAACAACCACCTCCGCCTATGAAGCCCGCCCG\n")
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17 f.write("AGTTACCATGCCCAGCATTAACCCCCCTCAACAACCACCTCCGCCTATGAAGCCCGCCCG\n")
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18 expFileName = "exp.classif"
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19 with open(expFileName, "w") as f:
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20 f.write("dummySSR\t120\t.\tok\tNA\tSSR\tNA\tCI=100; struct=(TElength: <150bps; SSRCoverage=0.00)\n")
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21 obsFileName = "%s.classif" % projectName
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22 statsFileName = "%s.classif_stats.txt" % projectName
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23 analysisFileName = "%s.SSR.set" % inputFileName
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24
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25 iTEclassifierPE = TEclassifierPE(inputFileName, configFileName, doClean = True)
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26 iTEclassifierPE.run()
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27
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28 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
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29
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30 iDb = DbFactory.createInstance()
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31 iDb.dropTable("%s_TR_set" % projectName)
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32 iDb.dropTable("%s_polyA_set" % projectName)
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33 iDb.dropTable("%s_ORF_map" % projectName)
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34 iDb.dropTable("%s_SSR_set" % projectName)
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35 iDb.close()
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36 os.remove(configFileName)
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37 os.remove(inputFileName)
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38 os.remove(expFileName)
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39 os.remove(obsFileName)
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40 os.remove(statsFileName)
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41 os.remove(analysisFileName)
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42
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43 def writeConfigFile(self, fileName, projectName):
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44 with open(fileName, "w") as f:
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45 f.write("[repet_env]\n")
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46 f.write("repet_host: %s\n" % os.environ["REPET_HOST"])
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47 f.write("repet_user: %s\n" % os.environ["REPET_USER"])
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48 f.write("repet_pw: %s\n" % os.environ["REPET_PW"])
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49 f.write("repet_db: %s\n" % os.environ["REPET_DB"])
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50 f.write("repet_port: %s\n" % os.environ["REPET_PORT"])
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51 f.write("\n")
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52 f.write("[project]\n")
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53 f.write("project_name: %s\n" % projectName)
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54 f.write("project_dir: %s\n" % os.getcwd())
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55 f.write("\n")
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56 f.write("[detect_features]\n")
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57 f.write("clean: yes\n")
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58 f.write("blast: ncbi\n")
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59 f.write("term_rep: no\n")
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60 f.write("polyA: no\n")
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61 f.write("tand_rep: yes\n")
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62 f.write("orf: no\n")
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63 f.write("TE_HMMER: no\n")
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64 f.write("TE_BLRtx: no\n")
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65 f.write("TE_BLRn: no\n")
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66 f.write("TE_BLRx: no\n")
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67 f.write("HG_BLRn: no\n")
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68 f.write("rDNA_BLRn: no\n")
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69 f.write("tRNA_scan: no\n")
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70 f.write("TRFmaxPeriod: 15\n")
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71 f.write("\n")
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72 f.write("[classif_consensus]\n")
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73 f.write("max_profiles_evalue: 1e-3\n")
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74 f.write("min_TE_profiles_coverage: 20\n")
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75 f.write("min_HG_profiles_coverage: 75\n")
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76 f.write("max_helitron_extremities_evalue: 1e-3\n")
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77 f.write("min_TE_bank_coverage: 5\n")
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78 f.write("min_HG_bank_coverage: 95\n")
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79 f.write("min_rDNA_bank_coverage: 95\n")
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80 f.write("min_HG_bank_identity: 90\n")
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81 f.write("min_rDNA_bank_identity: 90\n")
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82 f.write("min_SSR_coverage: 0.75\n")
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83 f.write("max_SSR_size: 150\n")
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84 f.write("clean: yes\n")
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85
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86 if __name__ == "__main__":
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87 unittest.main() |
