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