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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 glycan_sets as gs
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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 self.kcinput = {"ringsmcaw": """ENTRY G04845 Glycan
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12 COMPOSITION (Gal)3 (Glc)1 (GlcNAc)2 (LFuc)2 (Neu5Ac)1
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13 MASS 1656.5
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14 DBLINKS CCSD: 23949
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15 GlycomeDB: 20420
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16 JCGGDB: JCGG-STR011245
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17 NODE 9
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18 1 Glc 0 0
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19 2 Gal -10 0
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20 3 GlcNAc -20 10
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21 4 GlcNAc -20 -10
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22 5 Gal -30 15
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23 6 LFuc -30 5
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24 7 LFuc -30 -5
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25 8 Gal -30 -15
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26 9 Neu5Ac -40 15
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27 EDGE 8
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28 1 2:b1 1:4
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29 2 3:b1 2:6
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30 3 4:b1 2:3
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31 4 5:b1 3:4
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32 5 6:a1 3:3
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33 6 7:a1 4:4
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34 7 8:b1 4:3
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35 8 9:a2 5:3
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36 ///
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37 ENTRY G05108 Glycan
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38 COMPOSITION (Gal)2 (GalNAc)1 (GlcNAc)1 (LFuc)1 (Neu5Ac)1 (S)1
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39 MASS 1266.2
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40 CLASS Glycoprotein; O-Glycan
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41 DBLINKS CCSD: 33353
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42 GlycomeDB: 20590
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43 JCGGDB: JCGG-STR011425
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44 NODE 7
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45 1 GalNAc 20 1
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46 2 Gal 10 1
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47 3 GlcNAc 0 1
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48 4 S -5 5
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49 5 Gal -10 1
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50 6 LFuc -10 -4
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51 7 Neu5Ac -20 1
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52 EDGE 6
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53 1 2:b1 1:3
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54 2 3:b1 2:3
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55 3 4 3:6
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56 4 5:b1 3:4
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57 5 6:a1 3:3
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58 6 7:a2 5:3
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59 ///
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60
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61 ENTRY G05121 Glycan
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62 COMPOSITION (Gal)2 (GalNAc)1 (GlcNAc)1 (LFuc)1 (Neu5Ac)2
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63 MASS 1477.3
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64 CLASS Glycoprotein; O-Glycan
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65 DBLINKS CCSD: 33350
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66 GlycomeDB: 20599
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67 JCGGDB: JCGG-STR011433
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68 NODE 7
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69 1 GalNAc 0 0
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70 2 Neu5Ac -10 5
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71 3 Gal -10 -5
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72 4 GlcNAc -20 -5
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73 5 Gal -30 0
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74 6 LFuc -30 -10
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75 7 Neu5Ac -40 0
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76 EDGE 6
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77 1 2:a2 1:6
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78 2 3:b1 1:3
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79 3 4:b1 3:3
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80 4 5:b1 4:4
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81 5 6:a1 4:3
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82 6 7:a2 5:3
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83 ///
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84
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85 ENTRY G04183 Glycan
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86 COMPOSITION (Gal)3 (GlcNAc)5 (LFuc)1 (Man)3 (Neu5Ac)3
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87 MASS 3026.8
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88 CLASS Glycoprotein; N-Glycan
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89 DBLINKS CCSD: 41981
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90 GlycomeDB: 19974
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91 JCGGDB: JCGG-STR010756
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92 NODE 15
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93 1 GlcNAc 0 0
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94 2 GlcNAc -10 0
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95 3 Man -20 0
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96 4 Man -30 10
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97 5 Man -30 -10
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98 6 GlcNAc -40 10
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99 7 GlcNAc -40 -5
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100 8 GlcNAc -40 -15
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101 9 Gal -50 10
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102 10 Gal -50 0
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103 11 LFuc -50 -10
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104 12 Gal -50 -15
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105 13 Neu5Ac -60 10
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106 14 Neu5Ac -60 0
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107 15 Neu5Ac -60 -15
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108 EDGE 14
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109 1 2:b1 1:4
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110 2 3:b1 2:4
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111 3 4:a1 3:6
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112 4 5:a1 3:3
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113 5 6:b1 4:2
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114 6 7:b1 5:4
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115 7 8:b1 5:2
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116 8 9:b1 6:4
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117 9 10:b1 7:4
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118 10 11:a1 7:3
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119 11 12:b1 8:4
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120 12 13:a2 9:6
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121 13 14:a2 10:3
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122 14 15:a2 12:6
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123 ///
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124
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125 ENTRY G04329 Glycan
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126 COMPOSITION (Gal)3 (GlcNAc)3 (LFuc)3 (Neu5Ac)1
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127 MASS 1843.7
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128 DBLINKS CCSD: 36620
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129 GlycomeDB: 20084
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130 JCGGDB: JCGG-STR010874
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131 NODE 10
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132 1 GlcNAc 27 -5
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133 2 Gal 18 0
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134 3 LFuc 18 -10
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135 4 GlcNAc 9 0
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136 5 Gal 0 5
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137 6 LFuc 0 -5
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138 7 GlcNAc -9 5
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139 8 Gal -18 10
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140 9 LFuc -18 0
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141 10 Neu5Ac -27 10
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142 EDGE 9
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143 1 2:b1 1:4
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144 2 3:a1 1:3
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145 3 4:b1 2:3
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146 4 5:b1 4:4
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147 5 6:a1 4:3
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148 6 7:b1 5:3
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149 7 8:b1 7:4
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150 8 9:a1 7:3
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151 9 10:a2 8:3
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152 ///
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153 ENTRY G04804 Glycan
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154 COMPOSITION (Gal)3 (GlcNAc)5 (LFuc)1 (Man)3 (Neu5Ac)3
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155 MASS 3026.8
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156 CLASS Glycoprotein; N-Glycan
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157 REFERENCE 1 [PMID:6704968]
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158 Chandrasekaran EV, Davila M, Nixon D, Mendicino J.
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159 Structures of the oligosaccharide chains of two forms of alpha 1-acid glycoprotein purified from liver metastases of lung, colon, and breast tumors.
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160 Cancer. Res. 44 (1984) 1557-67.
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161 DBLINKS CCSD: 8168
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162 GlycomeDB: 33225
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163 JCGGDB: JCGG-STR024138
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164 NODE 15
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165 1 GlcNAc 27.2 1.6
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166 2 GlcNAc 17.2 1.6
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167 3 Man 8.2 1.6
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168 4 Man 0.2 7.6
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169 5 Man 0.2 -4.4
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170 6 GlcNAc -8.8 7.6
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171 7 GlcNAc -8.8 -0.4
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172 8 GlcNAc -8.8 -8.4
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173 9 Gal -17.8 7.6
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174 10 Gal -17.8 3.6
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175 11 LFuc -17.8 -4.4
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176 12 Gal -17.8 -8.4
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177 13 Neu5Ac -26.8 7.6
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178 14 Neu5Ac -26.8 3.6
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179 15 Neu5Ac -26.8 -8.4
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180 EDGE 14
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181 1 2:b1 1:4
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182 2 3:b1 2:4
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183 3 4:a1 3:6
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184 4 5:a1 3:3
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185 5 6:b1 4:2
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186 6 7:b1 5:4
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187 7 8:b1 5:2
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188 8 9:b1 6:4
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189 9 10:b1 7:4
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190 10 11:a1 7:3
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191 11 12:b1 8:4
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192 12 13:a2 9:3
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193 13 14:a2 10:3
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194 14 15:a2 12:6
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195 ///
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196 """, "ringsmcaw_modified": """ENTRY G04845 Glycan
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197 NODE 9
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198 1 Glc 0 0
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199 2 Gal -10 0
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200 3 GlcNAc -20 10
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201 4 GlcNAc -20 -10
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202 5 Gal -30 15
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203 6 LFuc -30 5
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204 7 LFuc -30 -5
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205 8 Gal -30 -15
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206 9 Neu5Ac -40 15
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207 EDGE 8
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208 1 2:b1 1:4
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209 2 3:b1 2:6
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210 3 4:b1 2:3
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211 4 5:b1 3:4
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212 5 6:a1 3:3
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213 6 7:a1 4:4
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214 7 8:b1 4:3
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215 8 9:a2 5:3
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216 ///
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217 ENTRY G05108 Glycan
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218 NODE 7
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219 1 GalNAc 20 1
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220 2 Gal 10 1
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221 3 GlcNAc 0 1
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222 4 S -5 5
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223 5 Gal -10 1
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224 6 LFuc -10 -4
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225 7 Neu5Ac -20 1
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226 EDGE 6
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227 1 2:b1 1:3
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228 2 3:b1 2:3
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229 3 4 3:6
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230 4 5:b1 3:4
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231 5 6:a1 3:3
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232 6 7:a2 5:3
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233 ///
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234 ENTRY G05121 Glycan
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235 NODE 7
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236 1 GalNAc 0 0
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237 2 Neu5Ac -10 5
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238 3 Gal -10 -5
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239 4 GlcNAc -20 -5
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240 5 Gal -30 0
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241 6 LFuc -30 -10
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242 7 Neu5Ac -40 0
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243 EDGE 6
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244 1 2:a2 1:6
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245 2 3:b1 1:3
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246 3 4:b1 3:3
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247 4 5:b1 4:4
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248 5 6:a1 4:3
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249 6 7:a2 5:3
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250 ///
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251 ENTRY G04183 Glycan
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252 NODE 15
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253 1 GlcNAc 0 0
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254 2 GlcNAc -10 0
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255 3 Man -20 0
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256 4 Man -30 10
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257 5 Man -30 -10
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258 6 GlcNAc -40 10
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259 7 GlcNAc -40 -5
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260 8 GlcNAc -40 -15
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261 9 Gal -50 10
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262 10 Gal -50 0
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263 11 LFuc -50 -10
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264 12 Gal -50 -15
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265 13 Neu5Ac -60 10
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266 14 Neu5Ac -60 0
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267 15 Neu5Ac -60 -15
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268 EDGE 14
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269 1 2:b1 1:4
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270 2 3:b1 2:4
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271 3 4:a1 3:6
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272 4 5:a1 3:3
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273 5 6:b1 4:2
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274 6 7:b1 5:4
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275 7 8:b1 5:2
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276 8 9:b1 6:4
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277 9 10:b1 7:4
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278 10 11:a1 7:3
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279 11 12:b1 8:4
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280 12 13:a2 9:6
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281 13 14:a2 10:3
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282 14 15:a2 12:6
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283 ///
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284 ENTRY G04329 Glycan
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285 NODE 10
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286 1 GlcNAc 27 -5
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287 2 Gal 18 0
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288 3 LFuc 18 -10
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289 4 GlcNAc 9 0
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290 5 Gal 0 5
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291 6 LFuc 0 -5
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292 7 GlcNAc -9 5
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293 8 Gal -18 10
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294 9 LFuc -18 0
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295 10 Neu5Ac -27 10
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296 EDGE 9
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297 1 2:b1 1:4
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298 2 3:a1 1:3
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299 3 4:b1 2:3
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300 4 5:b1 4:4
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301 5 6:a1 4:3
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302 6 7:b1 5:3
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303 7 8:b1 7:4
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304 8 9:a1 7:3
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305 9 10:a2 8:3
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306 ///
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307 ENTRY G04804 Glycan
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308 NODE 15
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309 1 GlcNAc 27.2 1.6
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310 2 GlcNAc 17.2 1.6
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311 3 Man 8.2 1.6
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312 4 Man 0.2 7.6
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313 5 Man 0.2 -4.4
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314 6 GlcNAc -8.8 7.6
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315 7 GlcNAc -8.8 -0.4
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316 8 GlcNAc -8.8 -8.4
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317 9 Gal -17.8 7.6
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318 10 Gal -17.8 3.6
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319 11 LFuc -17.8 -4.4
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320 12 Gal -17.8 -8.4
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321 13 Neu5Ac -26.8 7.6
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322 14 Neu5Ac -26.8 3.6
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323 15 Neu5Ac -26.8 -8.4
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324 EDGE 14
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325 1 2:b1 1:4
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326 2 3:b1 2:4
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327 3 4:a1 3:6
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328 4 5:a1 3:3
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329 5 6:b1 4:2
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330 6 7:b1 5:4
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331 7 8:b1 5:2
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332 8 9:b1 6:4
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333 9 10:b1 7:4
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334 10 11:a1 7:3
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335 11 12:b1 8:4
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336 12 13:a2 9:3
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337 13 14:a2 10:3
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338 14 15:a2 12:6
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339 ///
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340 """, "ringsfinger": """ENTRY G00015 Glycan
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341 NODE 8
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342 1 Asn 20 0
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343 2 GlcNAc 12 0
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344 3 GlcNAc 3 0
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345 4 Man -5 0
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346 5 Man -12 5
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347 6 Man -12 -5
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348 7 GlcNAc -20 5
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349 8 GlcNAc -20 -5
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350 EDGE 7
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351 1 2:b1 1
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352 2 3:b1 2:4
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353 3 4:b1 3:4
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354 4 5:a1 4:6
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355 5 6:a1 4:3
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356 6 7:b1 5:2
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357 7 8:b1 6:2
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358 ///
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359 ENTRY G00016 Glycan
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360 NODE 9
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361 1 Asn 20 3
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362 2 GlcNAc 12 3
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363 3 LFuc 4 8
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364 4 GlcNAc 3 -2
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365 5 Man -5 -2
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366 6 Man -12 3
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367 7 Man -12 -7
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368 8 GlcNAc -20 3
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369 9 GlcNAc -20 -7
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370 EDGE 8
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371 1 2:b1 1
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372 2 3:a1 2:6
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373 3 4:b1 2:4
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374 4 5:b1 4:4
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375 5 6:a1 5:6
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376 6 7:a1 5:3
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377 7 8:b1 6:2
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378 8 9:b1 7:2
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379 ///
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380 ENTRY G00017 Glycan
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381 NODE 11
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382 1 Asn 24 3
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383 2 GlcNAc 14 3
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384 3 LFuc 7 8
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385 4 GlcNAc 6 -2
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386 5 Man -2 -2
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387 6 Man -8 3
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388 7 Man -8 -7
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389 8 GlcNAc -16 3
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390 9 GlcNAc -16 -7
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391 10 Gal -24 3
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392 11 Gal -24 -7
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393 EDGE 10
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394 1 2:b1 1
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395 2 3:a1 2:6
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396 3 4:b1 2:4
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397 4 5:b1 4:4
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398 5 6:a1 5:6
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399 6 7:a1 5:3
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400 7 8:b1 6:2
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401 8 9:b1 7:2
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402 9 10:b1 8:4
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403 10 11:b1 9:4
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404 ///
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405 ENTRY G00018 Glycan
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406 NODE 13
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407 1 Asn 28 3
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408 2 GlcNAc 18 3
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409 3 LFuc 10 8
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410 4 GlcNAc 9 -2
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411 5 Man 1 -2
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412 6 Man -5 4
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413 7 Man -5 -8
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414 8 GlcNAc -13 4
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415 9 GlcNAc -13 -8
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416 10 Gal -21 4
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417 11 Gal -21 -8
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418 12 Neu5Ac -29 4
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419 13 Neu5Ac -29 -8
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420 EDGE 12
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421 1 2:b1 1
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422 2 3:a1 2:6
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423 3 4:b1 2:4
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424 4 5:b1 4:4
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425 5 6:a1 5:6
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426 6 7:a1 5:3
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427 7 8:b1 6:2
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428 8 9:b1 7:2
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429 9 10:b1 8:4
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430 10 11:b1 9:4
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431 11 12:a2 10:6
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432 12 13:a2 11:6
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433 ///
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434 ENTRY G00019 Glycan
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435 NODE 9
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436 1 Asn 20 0
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437 2 GlcNAc 12 0
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438 3 GlcNAc 3 0
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439 4 Man -5 0
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440 5 Man -12 5
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441 6 Man -12 -5
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442 7 GlcNAc -15 0
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443 8 GlcNAc -20 5
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444 9 GlcNAc -20 -5
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445 EDGE 8
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446 1 2:b1 1
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447 2 3:b1 2:4
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448 3 4:b1 3:4
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449 4 5:a1 4:6
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450 5 6:a1 4:3
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451 6 7:b1 4:4
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452 7 8:b1 5:2
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453 8 9:b1 6:2
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454 ///
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455 ENTRY G00020 Glycan
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456 NODE 9
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457 1 Asn 20 3
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458 2 GlcNAc 11 3
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459 3 GlcNAc 2 3
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460 4 Man -6 3
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461 5 Man -13 9
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462 6 Man -13 -3
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463 7 GlcNAc -21 9
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464 8 GlcNAc -21 2
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465 9 GlcNAc -21 -8
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466 EDGE 8
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467 1 2:b1 1
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468 2 3:b1 2:4
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469 3 4:b1 3:4
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470 4 5:a1 4:6
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471 5 6:a1 4:3
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472 6 7:b1 5:2
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473 7 8:b1 6:4
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474 8 9:b1 6:2
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475 ///
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|
476 """, "ringsbroken": """ABCDEFGENTRY G00015 Glycan
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477 NODE 8
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478 1 Asn 20 0
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|
479 2 GlcNAc 12 0
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|
480 """
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|
|
481 }
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482 os.environ["http_proxy"] = "" # work around for IOError: [Errno url error] invalid proxy for http:
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483 pass
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484
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485 def tearDown(self):
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486 pass
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487
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488 def test_broken_kcf(self):
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|
|
489 import StringIO
|
|
|
490
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491 brk = self.kcinput["ringsbroken"]
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|
|
492 handle = StringIO.StringIO(''.join(brk))
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|
493 with self.assertRaises(UnboundLocalError):
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494 gs.glycan_set_comparison(handle, handle)
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495
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496 def test_same_kcf(self):
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497 import StringIO
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498
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|
|
499 kcf = self.kcinput["ringsfinger"]
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|
500 handle = StringIO.StringIO(''.join(kcf))
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501 handle2 = StringIO.StringIO(''.join(kcf))
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502 uniquesetA, uniquesetB, union, intersection, AB, BA = gs.glycan_set_comparison(handle, handle2)
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503 self.assertEqual(uniquesetA, uniquesetB)
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|
504 self.assertEqual(union, intersection)
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|
505 self.assertEqual(AB, BA)
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|
|
506
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|
|
507 def test_diff_kcf(self):
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|
|
508 import StringIO
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|
|
509
|
|
|
510 kcf = self.kcinput["ringsfinger"]
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|
|
511 kcf2 = self.kcinput["ringsmcaw"]
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|
|
512 handle = StringIO.StringIO(''.join(kcf))
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|
|
513 handle2 = StringIO.StringIO(''.join(kcf2))
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|
|
514 uniquesetA, uniquesetB, union, intersection, AB, BA = gs.glycan_set_comparison(handle, handle2)
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|
|
515 self.assertNotEqual(uniquesetA, uniquesetB)
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|
516 self.assertNotEqual(union, intersection)
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|
|
517 self.assertNotEqual(AB, BA)
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|
518
|
|
|
519 def test_diff_kcf_modified(self):
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|
|
520 import StringIO
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|
521
|
|
|
522 kcf = self.kcinput["ringsfinger"]
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|
|
523 kcf2 = self.kcinput["ringsmcaw_modified"]
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|
|
524 handle = StringIO.StringIO(''.join(kcf))
|
|
|
525 handle2 = StringIO.StringIO(''.join(kcf2))
|
|
|
526 uniquesetA, uniquesetB, union, intersection, AB, BA = gs.glycan_set_comparison(handle, handle2)
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|
|
527 self.assertNotEqual(uniquesetA, uniquesetB)
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|
528 self.assertNotEqual(union, intersection)
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|
|
529 self.assertNotEqual(AB, BA)
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|
|
530
|
|
|
531 # def test_bug_read_kcf(self):
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|
|
532 # """
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|
|
533 # readkcf is not a full implementation. Fails on ringsmcaw test set
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|
|
534 # :return:
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|
|
535 # """
|
|
|
536 # import StringIO
|
|
|
537 #
|
|
|
538 # kcf = self.kcinput["ringsfinger"]
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|
|
539 # kcf2 = self.kcinput["ringsmcaw"]
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|
|
540 # handle = StringIO.StringIO(''.join(kcf))
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|
|
541 # handle2 = StringIO.StringIO(''.join(kcf2))
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|
|
542 # with self.assertRaises(ValueError):
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|
|
543 # uniquesetA, uniquesetB, union, intersection, AB, BA = gs.glycan_set_comparison(handle, handle2)
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|
|
544
|
|
|
545 def test_empty_stream(self):
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|
|
546 with self.assertRaises(IOError):
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|
|
547 uniquesetA, uniquesetB, union, intersection, AB, BA = gs.glycan_set_comparison("", "")
|
|
|
548 with self.assertRaises(IOError):
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|
|
549 uniquesetA, uniquesetB, union, intersection, AB, BA = gs.glycan_set_comparison([], [])
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|
|
550 with self.assertRaises(IOError):
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|
551 uniquesetA, uniquesetB, union, intersection, AB, BA = gs.glycan_set_comparison(None, None)
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|
|
552
|
|
|
553
|
|
|
554 def run_tests():
|
|
|
555 unittest.main()
|
|
|
556
|
|
|
557
|
|
|
558 if __name__ == '__main__':
|
|
|
559 run_tests()
|
