Mercurial > repos > yufei-luo > s_mart

comparison commons/pyRepetUnit/hmmer/tests/TestHmmpfamClusterComponent.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 import ConfigParser
4 import commons.pyRepetUnit.hmmer.HmmpfamClusterComponent
5 from pyRepet.sql.RepetJobMySQL import *
6 from pyRepet.util.file.FileUtils import *
7
8 class TestHmmpfamClusterComponent(unittest.TestCase):
9
10 def setUp(self):
11
12 self.component = commons.pyRepetUnit.hmmer.HmmpfamClusterComponent.HmmpfamClusterComponent()
13
14 def testLoadConfig(self):
15 config = open("tmpConfig.cfg", "w")
16 config.write("[profil_search]\n")
17 config.write("ProfilDatabank: /repet_pipe/commons/pyRepetUnit/hmmer/datas/myhmms\n")
18 config.write("[hmmer_config]\n")
19 config.write("result_dir: /repet_results\n")
20 config.write("query_dir: /repet_datas/hmmer_in_parallel\n")
21 config.write("tmp_dir: /repet_tmp\n")
22 config.write("[sge_config]\n")
23 config.write("queue: main.q\n")
24 config.write("groupid: fake\n")
25 config.close()
26 config = ConfigParser.ConfigParser()
27 config.readfp( open("tmpConfig.cfg") )
28 self.component.loadConfig(config)
29 self.assertEquals( "/repet_pipe/commons/pyRepetUnit/hmmer/datas/myhmms", self.component.getProfilDatabank() )
30 self.assertEquals( "/repet_results", self.component.getResultDir() )
31 self.assertEquals( "/repet_datas/hmmer_in_parallel", self.component.getQueryDir() )
32 self.assertEquals( "/repet_tmp", self.component.getTmpDir() )
33 self.assertEquals( "main.q", self.component.getSGEQueue() )
34 self.assertEquals( "fake", self.component.getSGEGroupId() )
35 os.system("rm tmpConfig.cfg")
36
37 def testClean (self):
38 fileUtils = FileUtils()
39 if (fileUtils.isRessourceExists("dummyTmpDir")):
40 os.system("rm -r dummyTmpDir")
41
42 if (fileUtils.isRessourceExists("dummyResultDir")):
43 os.system("rm -r dummyResultDir")
44
45 os.mkdir("dummyTmpDir")
46 os.system("touch dummyTmpDir/srptJob1_fake_HmmpfamJob1_2009-3-11_12394.py")
47 os.system("touch dummyTmpDir/srptJob2_fake_HmmpfamJob1_2009-3-11_12394.py")
48 os.system("touch dummyTmpDir/srptJob3_fake_HmmpfamJob1_2009-3-11_12394.py")
49 os.system("touch dummyTmpDir/srptJob4_fake_HmmpfamJob1_2009-3-11_12394.py")
50
51 os.mkdir("dummyResultDir")
52 os.system("touch dummyResultDir/batch_1.fa.hmmpfamOut")
53 os.system("touch dummyResultDir/batch_2.fa.hmmpfamOut")
54 os.system("touch dummyResultDir/batch_3.fa.hmmpfamOut")
55 os.system("touch dummyResultDir/batch_4.fa.hmmpfamOut")
56
57 self.component.setTmpDir("dummyTmpDir")
58 self.component.setResultDir("dummyResultDir")
59
60 self.component.clean()
61
62 self.assertFalse(fileUtils.isRessourceExists("dummyTmpDir/srptJob1_fake_HmmpfamJob1_2009-3-11_12394.py"))
63 self.assertFalse(fileUtils.isRessourceExists("dummyTmpDir/srptJob1_fake_HmmpfamJob2_2009-3-11_12394.py"))
64 self.assertFalse(fileUtils.isRessourceExists("dummyTmpDir/srptJob1_fake_HmmpfamJob3_2009-3-11_12394.py"))
65 self.assertFalse(fileUtils.isRessourceExists("dummyTmpDir/srptJob1_fake_HmmpfamJob4_2009-3-11_12394.py"))
66 self.assertFalse(fileUtils.isRessourceExists("dummyResultDir/batch_1.fa.hmmpfamOut"))
67 self.assertFalse(fileUtils.isRessourceExists("dummyResultDir/batch_2.fa.hmmpfamOut"))
68 self.assertFalse(fileUtils.isRessourceExists("dummyResultDir/batch_3.fa.hmmpfamOut"))
69 self.assertFalse(fileUtils.isRessourceExists("dummyResultDir/batch_4.fa.hmmpfamOut"))
70
71 os.system("rm -r dummyTmpDir")
72 os.system("rm -r dummyResultDir")
73
74
75 if __name__ == "__main__":
76 unittest.main()