Mercurial > repos > yufei-luo > s_mart

comparison commons/tools/tests/Test_GetMultAlignAndPhylogenyPerTErefSeq.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 unittest
2 import os
3 import time
4 from commons.core.sql.DbMySql import DbMySql
5 from commons.tools.GetMultAlignAndPhylogenyPerTErefSeq import GetMultAlignAndPhylogenyPerTErefSeq
6 from commons.core.utils.FileUtils import FileUtils
7
8
9 class Test_GetMultAlignAndPhylogenyPerTErefSeq( unittest.TestCase ):
10
11 def setUp( self ):
12 self.fileUtils = FileUtils()
13 self._inputTEFile = "dummyTE"
14 self._iGMAP = GetMultAlignAndPhylogenyPerTErefSeq()
15 self._uniqId = "%s_%s" % ( time.strftime("%Y_%m_%d_%H_%M_%S") , os.getpid() )
16 self._configFileName = "dummyConfig_%s" % self._uniqId
17 configFile = open( self._configFileName, "w" )
18 configFile.write("[repet_env]\n")
19 configFile.write( "repet_host: %s\n" % ( os.environ["REPET_HOST"] ) )
20 configFile.write( "repet_user: %s\n" % ( os.environ["REPET_USER"] ) )
21 configFile.write( "repet_pw: %s\n" % ( os.environ["REPET_PW"] ) )
22 configFile.write( "repet_db: %s\n" % ( os.environ["REPET_DB"] ) )
23 configFile.write( "repet_port: %s\n" % ( os.environ["REPET_PORT"] ) )
24 configFile.close()
25
26 def tearDown( self ):
27 os.remove( self._configFileName )
28 os.remove( self._inputTEFile )
29
30
31 def test_getNamesOfTErefSeq_fromFile_ok(self):
32 expTEList =["DHX-incomp-chim_Blc1_DmelChr4-L-B1-Map1_reversed",
33 "DT-comp_DmelChr4-B-P0.0-Map3", "RLX-incomp_Blc3_DmelChr4-L-B3-Map1"]
34 self._iGMAP._TErefseq = os.path.abspath(self._inputTEFile)
35 self.writeInputTEFile()
36 obsTEList = self._iGMAP.getNamesOfTErefSeq()
37 self.assertEqual(obsTEList, expTEList)
38
39 def test_getNamesOfTErefSeq_from_empty_file(self):
40 expTEList =[]
41 self._iGMAP._TErefseq = os.path.abspath(self._inputTEFile)
42 with open(self._inputTEFile,"w") as TEFile:
43 TEFile.write("")
44 obsTEList = self._iGMAP.getNamesOfTErefSeq()
45 self.assertEqual(obsTEList, expTEList)
46
47 def writeInputTEFile(self):
48 with open(self._inputTEFile,"w") as TEFile:
49 TEFile.write("""DHX-incomp-chim_Blc1_DmelChr4-L-B1-Map1_reversed
50 RLX-incomp_Blc3_DmelChr4-L-B3-Map1\t reverse
51 DT-comp_DmelChr4-B-P0.0-Map3\t""")
52
53 if __name__ == "__main__":
54 unittest.main()