Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/coord/test/Test_Path.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 # Copyright INRA (Institut National de la Recherche Agronomique) |
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2 # http://www.inra.fr |
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3 # http://urgi.versailles.inra.fr |
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4 # |
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5 # This software is governed by the CeCILL license under French law and |
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6 # abiding by the rules of distribution of free software. You can use, |
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7 # modify and/ or redistribute the software under the terms of the CeCILL |
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8 # license as circulated by CEA, CNRS and INRIA at the following URL |
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9 # "http://www.cecill.info". |
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10 # |
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11 # As a counterpart to the access to the source code and rights to copy, |
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12 # modify and redistribute granted by the license, users are provided only |
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13 # with a limited warranty and the software's author, the holder of the |
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14 # economic rights, and the successive licensors have only limited |
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15 # liability. |
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16 # |
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17 # In this respect, the user's attention is drawn to the risks associated |
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18 # with loading, using, modifying and/or developing or reproducing the |
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19 # software by the user in light of its specific status of free software, |
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20 # that may mean that it is complicated to manipulate, and that also |
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21 # therefore means that it is reserved for developers and experienced |
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22 # professionals having in-depth computer knowledge. Users are therefore |
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23 # encouraged to load and test the software's suitability as regards their |
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24 # requirements in conditions enabling the security of their systems and/or |
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25 # data to be ensured and, more generally, to use and operate it in the |
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26 # same conditions as regards security. |
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27 # |
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28 # The fact that you are presently reading this means that you have had |
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29 # knowledge of the CeCILL license and that you accept its terms. |
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30 |
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31 |
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32 import unittest |
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33 from commons.core.coord.Path import Path |
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34 from commons.core.coord.Align import Align |
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35 from commons.core.coord.Set import Set |
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36 |
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37 |
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38 class Test_Path( unittest.TestCase ): |
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39 |
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40 def setUp( self ): |
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41 self._path = Path() |
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42 |
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43 def test_setFromTuple( self ): |
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44 line = "1\tchr1\t1\t10\tTE2\t11\t17\t1e-20\t30\t90.2" |
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45 self._path.setFromTuple( line.split("\t") ) |
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46 self.assertEqual( self._path.id, 1 ) |
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47 self.assertEqual( self._path.range_query.seqname, "chr1" ) |
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48 self.assertEqual( self._path.range_query.start, 1 ) |
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49 self.assertEqual( self._path.range_query.end, 10 ) |
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50 self.assertEqual( self._path.range_subject.seqname, "TE2" ) |
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51 self.assertEqual( self._path.range_subject.start, 11 ) |
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52 self.assertEqual( self._path.range_subject.end, 17 ) |
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53 self.assertEqual( self._path.e_value, float("1e-20") ) |
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54 self.assertEqual( self._path.score, float("30") ) |
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55 self.assertEqual( self._path.identity, float("90.2") ) |
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56 |
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57 def test___eq__( self ): |
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58 self._path.setFromString( "1\tchr1\t1\t6\tTE2\t11\t16\t1e-20\t30\t90.2\n" ) |
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59 o = Path() |
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60 o.setFromString( "1\tchr1\t1\t6\tTE2\t11\t16\t1e-20\t30\t90.2\n" ) |
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61 self.assertEqual( self._path, o ) |
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62 o.setFromString( "2\tchr1\t1\t6\tTE2\t11\t16\t1e-20\t30\t90.2\n" ) |
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63 self.assertNotEqual( self._path, o ) |
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64 o.setFromString( "1\tchr1\t1\t6\tTE2\t11\t16\t1e-20\t3000000\t90.2\n" ) |
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65 self.assertNotEqual( self._path, o ) |
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66 |
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67 def test_canMerge( self ): |
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68 tuple = ("1", "chr1","1", "10","TE2","11","17","1e-20","30","90.2") |
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69 self._path.setFromTuple(tuple) |
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70 tuple = ("2", "chr1","2", "9","TE2","10","13","1e-20","30","90.2") |
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71 o = Path() |
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72 o.setFromTuple(tuple) |
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73 self.assertTrue(self._path.canMerge(o)) |
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74 |
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75 def test_canMerge_on_same_id ( self ): |
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76 tuple = ("1", "chr1","1", "10","TE2","11","17","1e-20","30","90.2") |
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77 self._path.setFromTuple(tuple) |
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78 tuple = ("1", "chr1","2", "9","TE2","10","13","1e-20","30","90.2") |
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79 o = Path() |
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80 o.setFromTuple(tuple) |
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81 self.assertFalse(self._path.canMerge(o)) |
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82 |
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83 def test_canMerge_on_same_chr( self ): |
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84 tuple = ("1", "chr1","1", "10","TE2","11","17","1e-20","30","90.2") |
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85 self._path.setFromTuple(tuple) |
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86 tuple = ("2", "chr2","2", "9","TE2","10","13","1e-20","30","90.2") |
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87 o = Path() |
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88 o.setFromTuple(tuple) |
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89 self.assertFalse(self._path.canMerge(o)) |
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90 |
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91 def test_canMerge_on_diff_subj( self ): |
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92 tuple = ("1", "chr1","1", "10","TE2","11","17","1e-20","30","90.2") |
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93 self._path.setFromTuple(tuple) |
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94 tuple = ("2", "chr1","2", "9","TE3","10","13","1e-20","30","90.2") |
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95 o = Path() |
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96 o.setFromTuple(tuple) |
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97 self.assertFalse(self._path.canMerge(o)) |
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98 |
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99 def test_canMerge_on_queries_that_do_not_overlap( self ): |
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100 tuple = ("1", "chr1","5", "11","TE2","11","17","1e-20","30","90.2") |
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101 self._path.setFromTuple(tuple) |
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102 tuple = ("2", "chr1","1", "4","TE2","10","13","1e-20","30","90.2") |
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103 o = Path() |
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104 o.setFromTuple(tuple) |
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105 self.assertFalse(self._path.canMerge(o)) |
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106 |
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107 def test_canMerge_on_subjects_that_do_not_overlap( self ): |
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108 tuple = ("1", "chr1","1", "10","TE2","11","17","1e-20","30","90.2") |
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109 self._path.setFromTuple(tuple) |
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110 tuple = ("2", "chr1","2", "9","TE2","1","10","1e-20","30","90.2") |
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111 o = Path() |
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112 o.setFromTuple(tuple) |
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113 self.assertFalse(self._path.canMerge(o)) |
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114 |
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115 def test_getSubjectAsSetOfQuery( self ): |
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116 tuple = ("1","chr1","1","10","TE2","11","17","1e-20","30","90.2") |
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117 self._path.setFromTuple(tuple) |
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118 exp = Set(1,"TE2","chr1",1,10) |
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119 obs = self._path.getSubjectAsSetOfQuery() |
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120 self.assertEqual( exp, obs ) |
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121 |
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122 def test_getSubjectAsSetOfQuery_on_neg_strand( self ): |
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123 tuple = ("1","chr1","10","1","TE2","11","17","1e-20","30","90.2") |
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124 self._path.setFromTuple(tuple) |
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125 exp = Set(1,"TE2","chr1",10,1) |
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126 obs = self._path.getSubjectAsSetOfQuery() |
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127 self.assertEqual( exp, obs ) |
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128 |
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129 def test_toString( self ): |
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130 self._path.setFromString( "1\tchr1\t1\t10\tTE3\t11\t17\t1e-20\t30\t85.2\n" ) |
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131 exp = "1\tchr1\t1\t10\tTE3\t11\t17\t%g\t30\t%f" % ( 1e-20, 85.2 ) |
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132 obs = self._path.toString() |
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133 self.assertEqual( obs, exp ) |
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134 |
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135 def test_getAlignInstance( self ): |
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136 self._path.setFromTuple( ( "2", "chr3", "250", "151", "seq5", "1", "100", "1e-32", "147", "87.9" ) ) |
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137 expAlign = Align() |
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138 expAlign.setFromTuple( ( "chr3", "151", "250", "seq5", "100", "1", "1e-32", "147", "87.9" ) ) |
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139 obsAlign = self._path.getAlignInstance() |
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140 self.assertEqual( expAlign, obsAlign ) |
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141 |
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142 |
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143 test_suite = unittest.TestSuite() |
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144 test_suite.addTest( unittest.makeSuite( Test_Path ) ) |
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145 if __name__ == "__main__": |
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146 unittest.TextTestRunner(verbosity=2).run( test_suite ) |