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1 __license__ = "MIT"
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2
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3 import unittest
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4 import rename_kcf as rk
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5
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6
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7 class SimpleUnitTest(unittest.TestCase):
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8 def setUp(self):
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9 import os
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10
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11 os.environ["http_proxy"] = "" # work around for IOError: [Errno url error] invalid proxy for http:
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12 pass
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13
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14 def tearDown(self):
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15 pass
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16
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17 def test_simple_kcf(self):
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18 import StringIO
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19
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20 kcinput = """ENTRY ((A??)AN) Glycan
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21 NODE 2
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22 1 galnac 0 0
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23 2 gal -8 0
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24 EDGE 1
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25 1 2:1 1
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26 ///
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27 """
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28
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29 kchandle = StringIO.StringIO(''.join(kcinput))
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30 h = rk.read_meta_kcf(kchandle)
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31 i = rk.flatten_meta_kcf_list(h)
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32 self.assertIn("ENTRY GLY0 Glycan\n", i)
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33
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34 def test_simple_kcf_rename_newcount(self):
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35 import StringIO
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36
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37 kcinput = """ENTRY ((A??)AN) Glycan
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38 NODE 2
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39 1 galnac 0 0
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40 2 gal -8 0
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41 EDGE 1
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42 1 2:1 1
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43 ///
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44 """
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45
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46 kchandle = StringIO.StringIO(''.join(kcinput))
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47 h = rk.read_meta_kcf(kchandle, "FLY", 15)
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48 i = rk.flatten_meta_kcf_list(h)
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49 self.assertIn("ENTRY FLY15 Glycan\n", i)
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50
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51 def test_initial_newline_simple_kcf(self):
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52 import StringIO
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53
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54 kcinput = """
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55 ENTRY ((A??)AN) Glycan
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56 NODE 2
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57 1 galnac 0 0
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58 2 gal -8 0
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59 EDGE 1
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60 1 2:1 1
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61 ///
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62 """
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63
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64 kchandle = StringIO.StringIO(''.join(kcinput))
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65 h = rk.read_meta_kcf(kchandle)
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66 i = rk.flatten_meta_kcf_list(h)
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67 self.assertIn("ENTRY GLY0 Glycan\n", i)
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68
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69 def test_multiple_kcf(self):
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70 import StringIO
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71
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72 kcinput = """ENTRY ((A??)AN) Glycan
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73 NODE 2
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74 1 galnac 0 0
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75 2 gal -8 0
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76 EDGE 1
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77 1 2:1 1
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78 ///
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79 ENTRY ((A??)AN) Glycan
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80 NODE 2
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81 1 galnac 0 0
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82 2 gal -8 0
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83 EDGE 1
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84 1 2:1 1
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85 ///
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86 ENTRY G00005 Glycan
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87 NODE 6
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88 1 PP-Dol 15 1
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89 2 GlcNAc 8 1
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90 3 GlcNAc 0 1
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91 4 Man -9 1
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92 5 Man -16 7
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93 6 Man -16 -6
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94 EDGE 5
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95 1 2:a1 1
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96 2 3:b1 2:4
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97 3 4:b1 3:4
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98 4 5:a1 4:6
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99 5 6:a1 4:3
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100 ///
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101 """
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102 kchandle = StringIO.StringIO(''.join(kcinput))
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103 h = rk.read_meta_kcf(kchandle)
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104 i = rk.flatten_meta_kcf_list(h)
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105 self.assertIn("ENTRY GLY0 Glycan\n", i)
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106 self.assertIn("ENTRY GLY1 Glycan\n", i)
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107 self.assertIn("ENTRY GLY2 Glycan\n", i)
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108
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109 def test_empty_stream(self):
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110 with self.assertRaises(IOError):
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111 m = rk.read_meta_kcf(None)
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112 with self.assertRaises(IOError):
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113 m = rk.read_meta_kcf([])
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114 with self.assertRaises(IOError):
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115 m = rk.read_meta_kcf("")
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116
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117 def test_non_integer_counter(self):
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118 import StringIO
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119
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120 kcinput = """ENTRY ((A??)AN) Glycan
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121 NODE 2
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122 1 galnac 0 0
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123 2 gal -8 0
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124 EDGE 1
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125 1 2:1 1
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126 ///
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127 """
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128
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129 kchandle = StringIO.StringIO(''.join(kcinput))
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130 with self.assertRaises(TypeError):
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131 h = rk.read_meta_kcf(kchandle, "FLY", "abc")
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132
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133
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134 def run_tests():
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135 unittest.main()
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136
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137
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138 if __name__ == '__main__':
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139 run_tests()
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140
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141
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