Mercurial > repos > yufei-luo > s_mart

comparison commons/tools/tests/Test_getCumulLengthFromTEannot.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.getCumulLengthFromTEannot import getCumulLengthFromTEannot
6 from commons.core.utils.FileUtils import FileUtils
7
8
9 class Test_getCumulLengthFromTEannot( unittest.TestCase ):
10
11 def setUp( self ):
12 self.fileUtils = FileUtils()
13 self._getCumulLengthFromTEannot = None
14 self._uniqId = "%s_%s" % ( time.strftime("%Y_%m_%d_%H_%M_%S") , os.getpid() )
15 self._configFileName = "dummyConfig_%s" % self._uniqId
16 configFile = open( self._configFileName, "w" )
17 configFile.write("[repet_env]\n")
18 configFile.write( "repet_host: %s\n" % ( os.environ["REPET_HOST"] ) )
19 configFile.write( "repet_user: %s\n" % ( os.environ["REPET_USER"] ) )
20 configFile.write( "repet_pw: %s\n" % ( os.environ["REPET_PW"] ) )
21 configFile.write( "repet_db: %s\n" % ( os.environ["REPET_DB"] ) )
22 configFile.write( "repet_port: %s\n" % ( os.environ["REPET_PORT"] ) )
23 configFile.close()
24
25
26 def tearDown( self ):
27 os.remove( self._configFileName )
28
29
30 def test_getAllSubjectsAsMapOfQueries( self ):
31 inFileName = "dummyInFile_%s" % self._uniqId
32 expFileName = "dummyExp_%s" % self._uniqId
33 for f in [inFileName,expFileName]:
34 if os.path.exists(f): os.remove(f)
35 inFile = open( inFileName, "w" )
36 inFile.write( "1\tchr1\t1501\t2500\tTE1\t1\t500\t0.0\t880\t95.7\n" )
37 inFile.write( "2\tchr1\t3401\t4000\tTE3\t101\t700\t0.0\t950\t97.2\n" )
38 inFile.close()
39 inTable = "dummyPathTable_%s" % self._uniqId
40 db = DbMySql(cfgFileName=self._configFileName)
41 db.createTable(inTable, "path", inFileName)
42 expFile = open( expFileName, "w" )
43 expFile.write( "TE1\tchr1\t1501\t2500\n" )
44 expFile.write( "TE3\tchr1\t3401\t4000\n" )
45 expFile.close()
46 self._getCumulLengthFromTEannot = getCumulLengthFromTEannot()
47 self._getCumulLengthFromTEannot._tableName = inTable
48 self._getCumulLengthFromTEannot._configFileName = self._configFileName
49 self._getCumulLengthFromTEannot.setAdaptatorToTable()
50 obsFileName = self._getCumulLengthFromTEannot.getAllSubjectsAsMapOfQueries()
51 self.assertTrue( self.fileUtils.are2FilesIdentical( obsFileName, expFileName ) )
52 for f in [inFileName,inTable+".map",expFileName]:
53 if os.path.exists(f): os.remove(f)
54 db.dropTable(inTable)
55 db.close()
56
57
58 def test_getCumulLength( self ):
59 mergeFileName = "dummyInFile_%s" % self._uniqId
60 mergeFile = open( mergeFileName, "w" )
61 mergeFile.write( "TE1\tchr1\t1501\t2500\n" )
62 mergeFile.write( "TE3\tchr1\t4000\t3401\n" )
63 mergeFile.close()
64 exp = 1000+600
65 self._getCumulLengthFromTEannot = getCumulLengthFromTEannot()
66 obs = self._getCumulLengthFromTEannot.getCumulLength( mergeFileName )
67 self.assertEqual( obs, exp )
68 os.remove( mergeFileName )
69
70 if __name__ == "__main__":
71 unittest.main()