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comparison commons/pyRepetUnit/convCoord/test/TestConvCoordWithOverlapps.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.utils.FileUtils import FileUtils
5 from commons.core.sql.DbMySql import DbMySql
6
7
8 class Test_ConvCoordWithOverlaps( unittest.TestCase ):
9 pass
10
11 # def setUp(self):
12 # self._uniqId = "%s_%s" % ( time.strftime("%Y%m%d%H%M%S") , os.getpid() )
13 # self._mapFile = "map_file.map"
14 # _MockMapFile( self._mapFile )
15 # self._resultFile = "dummyObsFile_%s" % ( self._uniqId )
16 # self._refFileToCompare = "dummyExpFile_%s" % ( self._uniqId )
17 # self._configFileName = "dummyConfigFile_%s" % ( self._uniqId )
18 # configF = open(self._configFileName, "w" )
19 # configF.write( "[repet_env]\n" )
20 # configF.write( "repet_host: %s\n" % ( os.environ["REPET_HOST"] ) )
21 # configF.write( "repet_user: %s\n" % ( os.environ["REPET_USER"] ) )
22 # configF.write( "repet_pw: %s\n" % ( os.environ["REPET_PW"] ) )
23 # configF.write( "repet_db: %s\n" % ( os.environ["REPET_DB"] ) )
24 # configF.write( "repet_port: %s\n" % ( os.environ["REPET_PORT"] ) )
25 # configF.close()
26 # self._db = DbMySql( cfgFileName = self._configFileName )
27 #
28 # def tearDown(self):
29 # os.remove( self._mapFile )
30 # os.remove( self._resultFile )
31 # os.remove( self._refFileToCompare )
32 # self._db.close()
33 # self._uniqId = None
34 #
35 #
36 # def test_run_TwoHitsOverlapOnFirstAndSecondChunks( self ):
37 # file2Process = "two_hits_overlap_on_first_and_second_chunk.align"
38 # linesToProcess = [ "chunk1" + "\t" + "95535" + "\t" + "95570" + "\t" + "sbj2" + "\t" + "125423" + "\t" + "125467" + "\t" + "7e-15" + "\t" + "82" + "\t" + "97.78" + "\n",
39 # "chunk2" + "\t" + "5544" + "\t" + "5575" + "\t" + "sbj2" + "\t" + "125457" + "\t" + "133465" + "\t" + "2e-38" + "\t" + "83" + "\t" + "65" + "\n" ]
40 # _MockAlignFile( file2Process, linesToProcess )
41 #
42 # convCoord = ConvCoord( file2Process, "q", self._mapFile, self._resultFile, "", 0, self._db )
43 # convCoord.run()
44 #
45 # refLine = ["dmel_chr4" + "\t" + "95535" + "\t" + "95575" + "\t" + "sbj2" + "\t" + "125423" + "\t" + "133465" + "\t" + "2e-38" + "\t" + "83" + "\t" + "97.78" + "\n"]
46 # _MockAlignFile( self._refFileToCompare, refLine )
47 #
48 # self.assertTrue( FileUtils.are2FilesIdentical( self._refFileToCompare, self._resultFile ) )
49 # os.remove( file2Process )
50 #
51 #
52 # def test_run_ThreeHitsOverlapOnFirstAndSecondChunks( self ):
53 # file2Process = "three_hits_overlap_on_first_and_second_chunk.align"
54 # linesToProcess = [ "chunk1" + "\t" + "95535" + "\t" + "95570" + "\t" + "sbj2" + "\t" + "125423" + "\t" + "125467" + "\t" + "7e-15" + "\t" + "82" + "\t" + "97.78" + "\n",
55 # "chunk2" + "\t" + "5544" + "\t" + "5575" + "\t" + "sbj2" + "\t" + "125457" + "\t" + "133465" + "\t" + "2e-38" + "\t" + "83" + "\t" + "65" + "\n"
56 # "chunk2" + "\t" + "5540" + "\t" + "5573" + "\t" + "sbj2" + "\t" + "125454" + "\t" +"125750" + "\t" + "8e-58" + "\t" + "224" + "\t" + "86.43" + "\n" ]
57 # _MockAlignFile( file2Process, linesToProcess )
58 #
59 # convCoord = ConvCoord( file2Process, "q", self._mapFile, self._resultFile, "", 0, self._db )
60 # convCoord.run()
61 #
62 # refLine = ["dmel_chr4" + "\t" + "95535" + "\t" + "95575" + "\t" + "sbj2" + "\t" + "125423" + "\t" + "133465" + "\t" + "8e-58" + "\t" + "224" + "\t" + "97.78" + "\n"]
63 # _MockAlignFile( self._refFileToCompare, refLine )
64 #
65 # self.assertTrue( FileUtils.are2FilesIdentical( self._refFileToCompare, self._resultFile ) )
66 # os.remove( file2Process )
67 #
68 #
69 # def test_run_HitsOnDifferentStrandsAndDifferentSubjects( self ):
70 # file2Process = "hits_on_different_strands_and_different_subjects.align"
71 # linesToProcess = [ "chunk1" + "\t" + "95535" + "\t" + "95570" + "\t" + "sbj2" + "\t" + "125423" + "\t" + "125467" + "\t" + "7e-15" + "\t" + "82" + "\t" + "97.78" + "\n",
72 # "chunk2" + "\t" + "5575" + "\t" + "5544" + "\t" + "sbj2" + "\t" + "125457" + "\t" + "133465" + "\t" + "2e-38" + "\t" + "83" + "\t" + "65" + "\n",
73 # "chunk2" + "\t" + "5540" + "\t" + "5573" + "\t" + "sbj3" + "\t" + "125454" + "\t" +"125750" + "\t" + "8e-58" + "\t" + "224" + "\t" + "86.43" + "\n" ]
74 # _MockAlignFile( file2Process, linesToProcess )
75 #
76 # convCoord = ConvCoord( file2Process, "q", self._mapFile, self._resultFile, "", 0, self._db )
77 # convCoord.run()
78 #
79 # refLine = ["dmel_chr4" + "\t" + "95535" + "\t" + "95570" + "\t" + "sbj2" + "\t" + "125423" + "\t" + "125467" + "\t" + "7e-15" + "\t" + "82" + "\t" + "97.78" + "\n",
80 # "dmel_chr4" + "\t" + "95544" + "\t" + "95575" + "\t" + "sbj2" + "\t" + "133465" + "\t" + "125457" + "\t" + "2e-38" + "\t" + "83" + "\t" + "65" + "\n",
81 # "dmel_chr4" + "\t" + "95540" + "\t" + "95573" + "\t" + "sbj3" + "\t" + "125454" + "\t" +"125750" + "\t" + "8e-58" + "\t" + "224" + "\t" + "86.43" + "\n" ]
82 # _MockAlignFile( self._refFileToCompare, refLine )
83 #
84 # self.assertTrue( FileUtils.are2FilesIdentical( self._refFileToCompare, self._resultFile ) )
85 # os.remove( file2Process )
86 #
87 #
88 # def test_run_TwoHitsOnChunksOnlyAndOnOverlap( self ):
89 # file2Process = "two_hits_on_chunks_only_and_on_overlap.align"
90 # linesToProcess = [ "chunk2" + "\t" + "85000" + "\t" + "95000" + "\t" + "sbj2" + "\t" + "125457" + "\t" + "133465" + "\t" + "2e-38" + "\t" + "83" + "\t" + "65" + "\n",
91 # "chunk3" + "\t" + "1000" + "\t" +" 5000" + "\t" + "sbj2" + "\t" + "125454" + "\t" + "125750" + "\t" + "8e-58" + "\t" + "224" + "\t" + "86.43" + "\n" ]
92 # _MockAlignFile( file2Process, linesToProcess )
93 #
94 # convCoord = ConvCoord( file2Process, "q", self._mapFile, self._resultFile, "", 0, self._db )
95 # convCoord.run()
96 #
97 # refLine = ["dmel_chr4" + "\t" + "175000"+ "\t" + "185000"+ "\t" + "sbj2"+ "\t" + "125454"+ "\t" + "133465"+ "\t" + "8e-58"+ "\t" + "224"+ "\t" + "86.43"+"\n"]
98 # _MockAlignFile( self._refFileToCompare, refLine )
99 #
100 # self.assertTrue( FileUtils.are2FilesIdentical( self._refFileToCompare, self._resultFile ) )
101 # os.remove( file2Process )
102 #
103 #
104 # def test_run_TwoHitsOnChunks_And_OnOverlap_OnReverseStrand_ForSubject( self ):
105 # file2Process = "two_hits_on_chunks_and_on_overlap_on_reverse_strand_for_subject.align"
106 # linesToProcess = [ "chunk2" + "\t" + "85000" + "\t" + "95000" + "\t" + "sbj2" + "\t" + "133465" + "\t" + "125457" + "\t" + "2e-38" + "\t" + "83" + "\t" + "65" + "\n",
107 # "chunk3" + "\t" + "1000" + "\t" + "5000" + "\t" + "sbj2" + "\t" + "125750" + "\t" + "125454" + "\t" + "8e-58" + "\t" + "224" + "\t" + "86.43" + "\n" ]
108 # _MockAlignFile( file2Process, linesToProcess )
109 #
110 # convCoord = ConvCoord( file2Process, "q", self._mapFile, self._resultFile, "", 0, self._db )
111 # convCoord.run()
112 #
113 # refLine = ["dmel_chr4" + "\t" + "175000"+ "\t" + "185000" + "\t" + "sbj2"+ "\t" + "133465" + "\t" + "125454" + "\t" + "8e-58"+ "\t" + "224"+ "\t" + "86.43"+"\n"]
114 # _MockAlignFile( self._refFileToCompare, refLine )
115 #
116 # self.assertTrue( FileUtils.are2FilesIdentical( self._refFileToCompare, self._resultFile ) )
117 # os.remove( file2Process )
118 #
119 #
120 # def test_run_ThreeHitsAllByAllWithTwoHitsWithinAChunkOverlap( self ):
121 # file2Process = "dummyAlignFile_%s" % ( self._uniqId )
122 # linesToProcess = [ "chunk1"+"\t"+"192"+"\t"+"197"+"\t"+"chunk2"+"\t"+"2"+"\t"+"7"+"\t"+"8e-58"+"\t"+"11"+"\t"+"97.8"+"\n",
123 # "chunk1"+"\t"+"192"+"\t"+"197"+"\t"+"chunk2"+"\t"+"51"+"\t"+"56"+"\t"+"8e-58"+"\t"+"11"+"\t"+"97.8"+"\n",
124 # "chunk2"+"\t"+"2"+"\t"+"7"+"\t"+"chunk2"+"\t"+"51"+"\t"+"56"+"\t"+"8e-58"+"\t"+"11"+"\t"+"97.8"+"\n" ]
125 # _MockAlignFile( file2Process, linesToProcess )
126 #
127 # mapFileName = "dummyMapFile_%s" % ( self._uniqId )
128 # mapF = open( mapFileName, "w" )
129 # mapF.write( "chunk1\tdmel_chr4\t1\t200\n" )
130 # mapF.write( "chunk2\tdmel_chr4\t191\t390\n" )
131 # mapF.close()
132 #
133 # convCoord = ConvCoord( file2Process, "qs", mapFileName, self._resultFile, "", 0, self._db )
134 # convCoord.run()
135 #
136 # refLine = [ "dmel_chr4"+"\t"+"192"+"\t"+"197"+"\t"+"dmel_chr4"+"\t"+"241"+"\t"+"246"+"\t"+"8e-58"+"\t"+"11"+"\t"+"97.8"+"\n" ]
137 # _MockAlignFile( self._refFileToCompare, refLine )
138 #
139 # self.assertTrue( FileUtils.are2FilesIdentical( self._refFileToCompare, self._resultFile ) )
140 # os.remove( file2Process )
141 # os.remove( mapFileName )
142 #
143 #
144 #class _MockAlignFile:
145 #
146 # def __init__(self, fileName, lines):
147 # alignF = open(fileName, "w");
148 # for line in lines:
149 # alignF.write(line)
150 # alignF.close
151 #
152 #
153 #class _MockMapFile:
154 #
155 # def __init__ (self, fileName):
156 # mapF = open(fileName, "w")
157 # line1 = "chunk1" + '\t' + "dmel_chr4" + '\t' + "1" + '\t'+ "100000" + "\n"
158 # line2 = "chunk2" + '\t' + "dmel_chr4" + '\t' + "90001" + '\t'+ "190000" + "\n"
159 # line3 = "chunk3" + '\t' + "dmel_chr4" + '\t' + "180001" + '\t' + "280000" + "\n"
160 # mapF.write(line1)
161 # mapF.write(line2)
162 # mapF.write(line3)
163 # mapF.close
164
165
166 test_suite = unittest.TestSuite()
167 test_suite.addTest( unittest.makeSuite( Test_ConvCoordWithOverlaps ) )
168 if __name__ == "__main__":
169 unittest.TextTestRunner(verbosity=2).run( test_suite )