Mercurial > repos > yufei-luo > s_mart
comparison commons/pyRepetUnit/hmmer/tests/TestHmmpfamClusterComponent.py @ 18:94ab73e8a190
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author | m-zytnicki |
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date | Mon, 29 Apr 2013 03:20:15 -0400 |
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17:b0e8584489e6 | 18:94ab73e8a190 |
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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() |