Mercurial > repos > yufei-luo > s_mart
comparison commons/pyRepetUnit/hmmer/tests/TestHmmpfamAndParse2alignLauncher.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 unittest | |
2 import os | |
3 import sys | |
4 | |
5 if not os.environ.has_key( "REPET_PATH" ): | |
6 print "*** Error: no environment variable REPET_PATH" | |
7 sys.exit(1) | |
8 sys.path.append( os.environ["REPET_PATH"] ) | |
9 | |
10 from pyRepet.launcher.Launcher import HmmpfamAndParse2alignLauncher | |
11 from pyRepet.sql.RepetJobMySQL import * | |
12 | |
13 class TestHmmpfamAndParse2alignLauncher(unittest.TestCase): | |
14 | |
15 def testConstructor(self): | |
16 | |
17 params = { | |
18 "query" : "toto", | |
19 "job_table":"fakeTable", | |
20 "queue" : "fakeQueue", | |
21 "groupid" : "fakeId", | |
22 "tmpDir" : "fakeDir", | |
23 "cDir" : "." | |
24 } | |
25 | |
26 hmmpfam = HmmpfamAndParse2alignLauncher("toto", params) | |
27 | |
28 self.assertEquals("toto", hmmpfam.query) | |
29 self.assertEquals("fakeTable", hmmpfam.job_table) | |
30 self.assertEquals("fakeQueue", hmmpfam.queue) | |
31 self.assertEquals("fakeId", hmmpfam.groupid) | |
32 self.assertEquals("fakeDir", hmmpfam.tmpdir) | |
33 | |
34 | |
35 def testCmd_start(self): | |
36 | |
37 fullInFileName = "/workspace/repet_pipe/commons/pyRepetUnit/hmmer/datas/test_input_aa.fa" | |
38 expectedCmdStart = "hmmpfam --informat FASTA -E 10 /workspace/repet_pipe/pyRepet/launcher/datas/hmmpfam/myhmms test_input_aa.fa > /workspace/repet_pipe/commons/pyRepetUnit/hmmer/datas/test_input_aa.fa.hmmpfamOut" | |
39 | |
40 user = "oinizan" | |
41 host = "pisano" | |
42 passwd = "oinizan" | |
43 dbName = "repet_oinizan" | |
44 jobDb = RepetJob(user , host , passwd , dbName) | |
45 params = {"param":"--informat FASTA -E 10", | |
46 "query" : "toto", | |
47 "job_table":"fake", | |
48 "queue" : "fake", | |
49 "groupid" : "fake", | |
50 "profilDB": "/workspace/repet_pipe/pyRepet/launcher/datas/hmmpfam/myhmms", | |
51 "tmpDir" : "fakeDir", | |
52 "outputDir": "/workspace/repet_pipe/commons/pyRepetUnit/hmmer/datas", | |
53 "scriptToLaunch": "/workspace/repet_pipe/repet_base/HmmpfamOutput2align_script.py", | |
54 "cDir" : "." | |
55 } | |
56 self.hmmpfam = HmmpfamAndParse2alignLauncher(jobDb, params) | |
57 self.assertEquals(expectedCmdStart, self.hmmpfam.cmd_start ( fullInFileName )) | |
58 | |
59 | |
60 def testCmd_finish(self): | |
61 | |
62 fullInFileName = "/workspace/repet_pipe/commons/pyRepetUnit/hmmer/datas/test_input_aa.fa" | |
63 user = "oinizan" | |
64 host = "pisano" | |
65 passwd = "oinizan" | |
66 dbName = "repet_oinizan" | |
67 jobDb = RepetJob(user , host , passwd , dbName) | |
68 params = {"param":"--informat FASTA -E 10", | |
69 "query" : "toto", | |
70 "job_table":"fake", | |
71 "queue" : "fake", | |
72 "groupid" : "fake", | |
73 "profilDB": "/workspace/repet_pipe/pyRepet/launcher/datas/hmmpfam/myhmms", | |
74 "tmpDir" : "fakeDir", | |
75 "outputDir": "/workspace/repet_pipe/commons/pyRepetUnit/hmmer/datas", | |
76 "scriptToLaunch": "/workspace/repet_pipe/repet_base/HmmpfamOutput2align_script.py", | |
77 "cDir" : "." | |
78 } | |
79 self.hmmpfamAndParse2align = HmmpfamAndParse2alignLauncher(jobDb, params) | |
80 expectedCmdFinish = "os.system( \"/workspace/repet_pipe/repet_base/HmmpfamOutput2align_script.py -i /workspace/repet_pipe/commons/pyRepetUnit/hmmer/datas/test_input_aa.fa.hmmpfamOut -o /workspace/repet_pipe/commons/pyRepetUnit/hmmer/datas/test_input_aa.fa.hmmpfamOut.align -c\" )\n" | |
81 self.assertEquals(expectedCmdFinish, self.hmmpfamAndParse2align.cmd_finish ( fullInFileName )) | |
82 | |
83 | |
84 | |
85 if __name__ == "__main__": | |
86 unittest.main() | |
87 |