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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 from commons.core.tree.Tree import Tree
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5 from commons.core.utils.FileUtils import FileUtils
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6
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7
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8 class Test_Tree( unittest.TestCase ):
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9
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10 def setUp( self ):
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11 self._tree = Tree()
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12 self._uniqId = "%s_%s" % ( time.strftime("%Y%m%d%H%M%S") , os.getpid() )
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13
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14
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15 def test_parseTree_oneLeaf( self ):
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16 inString = "seq1:0.0023"
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17 obs = self._tree.parseTree( inString )
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18 exp = { "left":None, "right":None, "name":"seq1", "length":0.0023 }
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19 self.assertEqual( obs, exp )
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20
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21
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22 def test_parseTree_twoLeaves( self ):
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23 inString = "(seq1:0.0023,seq2:0.0017)"
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24 obs = self._tree.parseTree( inString )
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25 exp = {'length':0, 'right':{'length':0.0016999999999999999, 'right':None, 'name':'seq2', 'left':None}, 'name':'internal', 'left':{'length':0.0023, 'right':None, 'name':'seq1', 'left':None}}
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26 self.assertEqual( obs, exp )
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27
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28 ## def test_parseTree_threeLeaves( self ):
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29 ## inString = "(seq1:0.0023,(seq2:0.0017,seq3:0.0009))"
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30 ## obs = self._tree.parseTree( inString )
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31 ## print obs
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32 ## exp = {'length':0, 'right':{'length':0.0016999999999999999, 'right':None, 'name':'seq2', 'left':None}, 'name':'internal', 'left':{'length':0.0023, 'right':None, 'name':'seq1', 'left':None}}
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33 ## self.assertEqual( obs, exp )
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34
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35
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36 def test_parseSubTree( self ):
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37 inString = "(seq1:0.0023,seq2:0.0017)"
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38 lExp = [ "seq1:0.0023", "seq2:0.0017" ]
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39 lObs = self._tree.parseSubTree( inString )
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40 self.assertEqual( lObs, lExp )
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41
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42
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43 def test_saveTree( self ):
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44 inFileName = "dummyInFile_%s" % ( self._uniqId )
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45 inF = open( inFileName, "w" )
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46 inF.write( "(seq4:0.012511,(seq3:0.005340,seq2:0.002201))" )
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47 inF.close()
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48 self._tree = Tree( inFileName )
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49 obsFileName = "dummyObsFile_%s" % ( self._uniqId )
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50 self._tree.saveTree( obsFileName )
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51 self.assertTrue( FileUtils.are2FilesIdentical( obsFileName, inFileName ) )
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52 for f in [ inFileName, obsFileName ]:
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53 os.remove( f )
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54
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55
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56 def test_retrieveInitialSequenceHeaders( self ):
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57 inString = "(seq4:0.012511,(seq3:0.005340,seq2:0.002201))"
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58 self._tree.tree = self._tree.parseTree( inString )
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59 dNew2Init = { "seq2":"consensus524::215 dmel_chr4 142..765", "seq3":"DmelChr4-B-G387-MAP16", "seq4":"1360|1cl-3gr" }
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60 expFileName = "dummyExpFile_%s" % ( self._uniqId )
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61 expF = open( expFileName, "w" )
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62 expF.write( "(1360|1cl-3gr:0.012511,(DmelChr4-B-G387-MAP16:0.005340,consensus524-215_dmel_chr4_142..765:0.002201))" )
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63 expF.close()
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64 obsFileName = "dummyObsFile_%s" % ( self._uniqId )
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65 self._tree.retrieveInitialSequenceHeaders( dNew2Init, obsFileName )
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66 self.assertTrue( FileUtils.are2FilesIdentical( obsFileName, expFileName ) )
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67 for f in [ expFileName, obsFileName ]:
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68 os.remove( f )
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69
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70
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71 def test_getNbOfLeaves( self ):
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72 inString = "(seq4:0.012511,(seq3:0.005340,seq2:0.002201))"
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73 self._tree.tree = self._tree.parseTree( inString )
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74 exp = 3
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75 obs = self._tree.getNbOfLeaves()
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76 self.assertEqual( obs, exp )
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77
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78
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79 def test_getNbOfNodes( self ):
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80 inString = "(seq4:0.012511,(seq3:0.005340,seq2:0.002201))"
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81 self._tree.tree = self._tree.parseTree( inString )
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82 exp = 4
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83 obs = self._tree.getNbOfNodes()
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84 self.assertEqual( obs, exp )
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85
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86
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87 test_suite = unittest.TestSuite()
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88 test_suite.addTest( unittest.makeSuite( Test_Tree ) )
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89 if __name__ == "__main__":
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90 unittest.TextTestRunner(verbosity=2).run( test_suite )
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