Mercurial > repos > yufei-luo > s_mart
comparison commons/tools/tests/Test_OrientSequences.py @ 18:94ab73e8a190
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author | m-zytnicki |
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date | Mon, 29 Apr 2013 03:20:15 -0400 |
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17:b0e8584489e6 | 18:94ab73e8a190 |
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1 import unittest | |
2 import time | |
3 import os | |
4 from commons.core.utils.FileUtils import FileUtils | |
5 from commons.tools.OrientSequences import OrientSequences | |
6 | |
7 | |
8 class Test_OrientSequences( unittest.TestCase ): | |
9 | |
10 def setUp( self ): | |
11 self._i = OrientSequences () | |
12 self._uniqId = "%s_%s" % ( time.strftime("%Y%m%d%H%M%S"), os.getpid() ) | |
13 | |
14 | |
15 def tearDown( self ): | |
16 self._i = None | |
17 self._uniqId = None | |
18 | |
19 | |
20 def test_parseMummerOutput( self ): | |
21 inFileName = "dummyInFile_%s" % ( self._uniqId ) | |
22 inF = open( inFileName, "w" ) | |
23 inF.write( "> seq1\n" ) | |
24 inF.write( " seq2 20 1 20\n" ) | |
25 inF.write( "> seq1 Reverse\n" ) | |
26 inF.write( " seq2 100 1 100\n" ) | |
27 inF.write( " seq2 450 400 50\n" ) | |
28 inF.close() | |
29 dExp = { "direct": 1, "reverse": 2 } | |
30 self._i._verbose = 0 | |
31 dObs = self._i.parseMummerOutput( inFileName, "seq1", "seq2" ) | |
32 self.assertEqual( dObs, dExp ) | |
33 os.remove( inFileName ) | |
34 | |
35 | |
36 def test_getSequencesToReverseFromMatrix_2seq( self ): | |
37 lNewHeaders = [ "seq1", "seq2" ] | |
38 dMatrix = { "1_vs_2": { "direct": 1, "reverse": 2 } } | |
39 lExp = [ "seq2" ] | |
40 self._i._verbose = 0 | |
41 lObs = self._i.getSequencesToReverseFromMatrix( dMatrix, lNewHeaders ) | |
42 lExp.sort() | |
43 lObs.sort() | |
44 self.assertEqual( lObs, lExp ) | |
45 | |
46 | |
47 def test_getSequencesToReverseFromMatrix_3seq( self ): | |
48 lNewHeaders = [ "seq1", "seq2", "seq3" ] | |
49 dMatrix = { "1_vs_2": { "direct": 1, "reverse": 10 }, | |
50 "1_vs_3": { "direct": 10, "reverse": 1 }, | |
51 "2_vs_3": { "direct": 1, "reverse": 10 } } | |
52 lExp = [ "seq2" ] | |
53 self._i._verbose = 0 | |
54 lObs = self._i.getSequencesToReverseFromMatrix( dMatrix, lNewHeaders ) | |
55 lExp.sort() | |
56 lObs.sort() | |
57 self.assertEqual( lExp, lObs ) | |
58 | |
59 | |
60 def test_getSequencesToReverseFromMatrix_4seq( self ): | |
61 lNewHeaders = [ "seq1", "seq2", "seq3", "seq4" ] | |
62 dMatrix = { "1_vs_2": { "direct": 10, "reverse": 1 }, | |
63 "1_vs_3": { "direct": 1, "reverse": 10 }, | |
64 "1_vs_4": { "direct": 1, "reverse": 10 }, | |
65 "2_vs_3": { "direct": 1, "reverse": 10 }, | |
66 "2_vs_4": { "direct": 1, "reverse": 10 }, | |
67 "3_vs_4": { "direct": 1, "reverse": 2 } } | |
68 lExp = [ "seq3", "seq4" ] | |
69 self._i._verbose = 0 | |
70 lObs = self._i.getSequencesToReverseFromMatrix( dMatrix, lNewHeaders ) | |
71 lExp.sort() | |
72 lObs.sort() | |
73 self.assertEqual( lExp, lObs ) | |
74 | |
75 | |
76 def test_orientInputSequences( self ): | |
77 lSeqToOrient = [ "seq1" ] | |
78 tmpFileName = "dummyInFile_%s" % ( self._uniqId ) | |
79 tmpF = open( tmpFileName, "w" ) | |
80 tmpF.write( ">seq1\n" ) | |
81 tmpF.write( "ATGCGGTGCATG\n" ) | |
82 tmpF.write( ">seq2\n" ) | |
83 tmpF.write( "GGCGAAGTGAAA\n" ) | |
84 tmpF.close() | |
85 expFileName = "dummyExpFile_%s" % ( self._uniqId ) | |
86 expF = open( expFileName, "w" ) | |
87 expF.write( ">seq1 re-oriented\n" ) | |
88 expF.write( "CATGCACCGCAT\n" ) | |
89 expF.write( ">seq2\n" ) | |
90 expF.write( "GGCGAAGTGAAA\n" ) | |
91 expF.close() | |
92 obsFileName = "dummyObsFile_%s" % ( self._uniqId ) | |
93 self._i._verbose = 0 | |
94 self._i._outFileName = obsFileName | |
95 self._i.orientInputSequences( lSeqToOrient, tmpFileName ) | |
96 self.assertTrue( FileUtils.are2FilesIdentical( obsFileName, expFileName ) ) | |
97 for f in [ tmpFileName, expFileName, obsFileName ]: | |
98 os.remove( f ) | |
99 | |
100 if __name__ == "__main__": | |
101 unittest.main() |