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