Mercurial > repos > yufei-luo > s_mart

comparison commons/tools/tests/Test_F_TEclassifierPE.py @ 18:94ab73e8a190

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author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
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17:b0e8584489e6 18:94ab73e8a190
1 import os
2 import unittest
3 from commons.tools.TEclassifierPE import TEclassifierPE
4 from commons.core.utils.FileUtils import FileUtils
5 from commons.core.sql.DbFactory import DbFactory
6
7 class Test_F_TEclassifierPE(unittest.TestCase):
8
9 def test_run(self):
10 projectName = "dummy"
11 configFileName = "dummy.cfg"
12 self.writeConfigFile(configFileName, projectName)
13 inputFileName = "dummy.fa"
14 with open(inputFileName, "w") as f:
15 f.write(">dummySSR\n")
16 f.write("AGTTACCATGCCCAGCATTAACCCCCCTCAACAACCACCTCCGCCTATGAAGCCCGCCCG\n")
17 f.write("AGTTACCATGCCCAGCATTAACCCCCCTCAACAACCACCTCCGCCTATGAAGCCCGCCCG\n")
18 expFileName = "exp.classif"
19 with open(expFileName, "w") as f:
20 f.write("dummySSR\t120\t.\tok\tNA\tSSR\tNA\tCI=100; struct=(TElength: <150bps; SSRCoverage=0.00)\n")
21 obsFileName = "%s.classif" % projectName
22 statsFileName = "%s.classif_stats.txt" % projectName
23 analysisFileName = "%s.SSR.set" % inputFileName
24
25 iTEclassifierPE = TEclassifierPE(inputFileName, configFileName, doClean = True)
26 iTEclassifierPE.run()
27
28 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
29
30 iDb = DbFactory.createInstance()
31 iDb.dropTable("%s_TR_set" % projectName)
32 iDb.dropTable("%s_polyA_set" % projectName)
33 iDb.dropTable("%s_ORF_map" % projectName)
34 iDb.dropTable("%s_SSR_set" % projectName)
35 iDb.close()
36 os.remove(configFileName)
37 os.remove(inputFileName)
38 os.remove(expFileName)
39 os.remove(obsFileName)
40 os.remove(statsFileName)
41 os.remove(analysisFileName)
42
43 def writeConfigFile(self, fileName, projectName):
44 with open(fileName, "w") as f:
45 f.write("[repet_env]\n")
46 f.write("repet_host: %s\n" % os.environ["REPET_HOST"])
47 f.write("repet_user: %s\n" % os.environ["REPET_USER"])
48 f.write("repet_pw: %s\n" % os.environ["REPET_PW"])
49 f.write("repet_db: %s\n" % os.environ["REPET_DB"])
50 f.write("repet_port: %s\n" % os.environ["REPET_PORT"])
51 f.write("\n")
52 f.write("[project]\n")
53 f.write("project_name: %s\n" % projectName)
54 f.write("project_dir: %s\n" % os.getcwd())
55 f.write("\n")
56 f.write("[detect_features]\n")
57 f.write("clean: yes\n")
58 f.write("blast: ncbi\n")
59 f.write("term_rep: no\n")
60 f.write("polyA: no\n")
61 f.write("tand_rep: yes\n")
62 f.write("orf: no\n")
63 f.write("TE_HMMER: no\n")
64 f.write("TE_BLRtx: no\n")
65 f.write("TE_BLRn: no\n")
66 f.write("TE_BLRx: no\n")
67 f.write("HG_BLRn: no\n")
68 f.write("rDNA_BLRn: no\n")
69 f.write("tRNA_scan: no\n")
70 f.write("TRFmaxPeriod: 15\n")
71 f.write("\n")
72 f.write("[classif_consensus]\n")
73 f.write("max_profiles_evalue: 1e-3\n")
74 f.write("min_TE_profiles_coverage: 20\n")
75 f.write("min_HG_profiles_coverage: 75\n")
76 f.write("max_helitron_extremities_evalue: 1e-3\n")
77 f.write("min_TE_bank_coverage: 5\n")
78 f.write("min_HG_bank_coverage: 95\n")
79 f.write("min_rDNA_bank_coverage: 95\n")
80 f.write("min_HG_bank_identity: 90\n")
81 f.write("min_rDNA_bank_identity: 90\n")
82 f.write("min_SSR_coverage: 0.75\n")
83 f.write("max_SSR_size: 150\n")
84 f.write("clean: yes\n")
85
86 if __name__ == "__main__":
87 unittest.main()