Mercurial > repos > yufei-luo > s_mart

comparison commons/tools/tests/Test_srptTableOverlap.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 import pyRepet.sql.RepetDBMySQL
5 from commons.core.utils.FileUtils import FileUtils
6 from commons.tools import srptTableOverlap
7
8
9 class Test_srptTableOverlap( unittest.TestCase ):
10
11 def setUp(self):
12 self._uniqId = "%s_%s" % ( time.strftime("%Y%m%d%H%M%S") , os.getpid() )
13 self._db = pyRepet.sql.RepetDBMySQL.RepetDB( os.environ["REPET_USER"],
14 os.environ["REPET_HOST"],
15 os.environ["REPET_PW"],
16 os.environ["REPET_DB"] )
17
18
19 def test_getOverlapAllPaths(self):
20 qryFileName = "dummyQryFile_%s" % ( self._uniqId )
21 qryF = open( qryFileName, "w" )
22 qryF.write("1\tchr1\t1301\t2000\tTE2\t11\t17\t1e-20\t30\t90.2\n")
23 qryF.close()
24 qryTable = "dummyQryTable_%s" % ( self._uniqId )
25 self._db.create_table( self._db, qryTable, qryFileName, "path" )
26 sbjFileName = "dummySbjFile_%s" % ( self._uniqId )
27 sbjF = open( sbjFileName, "w" )
28 sbjF.write("1\tchr1\t1001\t1500\tTE1\t11\t17\t1e-20\t30\t90.2\n") # 200-bp overlap: 1301-1500
29 sbjF.write("2\tchr1\t1401\t1800\tTE2\t11\t17\t1e-20\t30\t90.2\n") # 300-bp overlap: 1501-1800
30 sbjF.write("3\tchr1\t2001\t2100\tTE2\t11\t17\t1e-20\t30\t90.2\n")
31 sbjF.write("4\tchr2\t1301\t2000\tTE2\t11\t17\t1e-20\t30\t90.2\n") # different query
32 sbjF.close()
33 sbjTable = "dummySbjTable_%s" % ( self._uniqId )
34 self._db.create_table( self._db, sbjTable, sbjFileName, "path" )
35 exp_sum_osize, exp_sum_non_osize, exp_sum_qsize = 500, 200, 700
36 obs_sum_osize, obs_sum_non_osize, obs_sum_qsize = srptTableOverlap.getOverlapAllPaths( qryTable, "path", sbjTable, "path", self._db )
37 self.assertEqual( obs_sum_osize, exp_sum_osize )
38 self.assertEqual( obs_sum_non_osize, exp_sum_non_osize )
39 self.assertEqual( obs_sum_qsize, exp_sum_qsize )
40 os.remove( qryFileName )
41 os.remove( sbjFileName )
42 self._db.remove_if_exist( qryTable )
43 self._db.remove_if_exist( sbjTable )
44
45
46 def test_pathOverlapByPath(self):
47 qryFileName = "dummyQryFile_%s" % ( self._uniqId )
48 qryF = open( qryFileName, "w" )
49 qryF.write("1\tchr1\t1301\t2000\tTE2\t1\t700\t1e-80\t850\t90.2\n")
50 qryF.write("1\tchr1\t2301\t3000\tTE2\t801\t1500\t1e-90\t930\t90.2\n")
51 qryF.close()
52 qryTable = "dummyQryTable_%s" % ( self._uniqId )
53 self._db.create_table( self._db, qryTable, qryFileName, "path" )
54 sbjFileName = "dummySbjFile_%s" % ( self._uniqId )
55 sbjF = open( sbjFileName, "w" )
56 sbjF.write("1\tchr1\t1401\t1800\tTE2\t11\t17\t1e-20\t30\t90.2\n")
57 sbjF.write("1\tchr1\t2101\t250000\tTE2\t11\t17\t1e-20\t30\t90.2\n")
58 sbjF.write("2\tchr1\t3501\t4000\tTE3\t11\t17\t1e-20\t30\t90.2\n")
59 sbjF.close()
60 sbjTable = "dummySbjTable_%s" % ( self._uniqId )
61 self._db.create_table( self._db, sbjTable, sbjFileName, "path" )
62 expFileName = "dummyOutFileExp_%s" % ( self._uniqId )
63 expF = open( expFileName, "w" )
64 expF.write("1\tTE2\t1400\t1:TE2\t1\t248300\t1100\t0.785714\t0.004430\n")
65 expF.close()
66 obsFileName = "dummyOutFileObs_%s" % ( self._uniqId )
67 obsF = open( obsFileName, "w" )
68 srptTableOverlap.pathOverlapByPath( qryTable, "path", sbjTable, "path", self._db, obsF )
69 obsF.close()
70 self.assertTrue( FileUtils.are2FilesIdentical( obsFileName, expFileName ) )
71 for f in [ qryFileName, sbjFileName, expFileName, obsFileName ]:
72 os.remove( f )
73 self._db.remove_if_exist( qryTable )
74 self._db.remove_if_exist( sbjTable )
75 self._db.remove_if_exist( sbjTable+"_bin" )
76
77
78 if __name__ == "__main__":
79 unittest.main()