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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 minimal_kcf as mk
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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 self.kcinput = {"ringsmcaw": """ENTRY G04845 Glycan
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11 COMPOSITION (Gal)3 (Glc)1 (GlcNAc)2 (LFuc)2 (Neu5Ac)1
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12 MASS 1656.5
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13 DBLINKS CCSD: 23949
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14 GlycomeDB: 20420
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15 JCGGDB: JCGG-STR011245
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16 NODE 9
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17 1 Glc 0 0
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18 2 Gal -10 0
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19 3 GlcNAc -20 10
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20 4 GlcNAc -20 -10
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21 5 Gal -30 15
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22 6 LFuc -30 5
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23 7 LFuc -30 -5
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24 8 Gal -30 -15
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25 9 Neu5Ac -40 15
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26 EDGE 8
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27 1 2:b1 1:4
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28 2 3:b1 2:6
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29 3 4:b1 2:3
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30 4 5:b1 3:4
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31 5 6:a1 3:3
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32 6 7:a1 4:4
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33 7 8:b1 4:3
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34 8 9:a2 5:3
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35 ///
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36 ENTRY G05108 Glycan
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37 COMPOSITION (Gal)2 (GalNAc)1 (GlcNAc)1 (LFuc)1 (Neu5Ac)1 (S)1
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38 MASS 1266.2
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39 CLASS Glycoprotein; O-Glycan
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40 DBLINKS CCSD: 33353
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41 GlycomeDB: 20590
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42 JCGGDB: JCGG-STR011425
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43 NODE 7
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44 1 GalNAc 20 1
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45 2 Gal 10 1
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46 3 GlcNAc 0 1
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47 4 S -5 5
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48 5 Gal -10 1
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49 6 LFuc -10 -4
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50 7 Neu5Ac -20 1
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51 EDGE 6
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52 1 2:b1 1:3
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53 2 3:b1 2:3
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54 3 4 3:6
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55 4 5:b1 3:4
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56 5 6:a1 3:3
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57 6 7:a2 5:3
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58 ///
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59
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60 ENTRY G05121 Glycan
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61 COMPOSITION (Gal)2 (GalNAc)1 (GlcNAc)1 (LFuc)1 (Neu5Ac)2
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62 MASS 1477.3
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63 CLASS Glycoprotein; O-Glycan
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64 DBLINKS CCSD: 33350
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65 GlycomeDB: 20599
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66 JCGGDB: JCGG-STR011433
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67 NODE 7
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68 1 GalNAc 0 0
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69 2 Neu5Ac -10 5
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70 3 Gal -10 -5
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71 4 GlcNAc -20 -5
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72 5 Gal -30 0
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73 6 LFuc -30 -10
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74 7 Neu5Ac -40 0
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75 EDGE 6
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76 1 2:a2 1:6
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77 2 3:b1 1:3
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78 3 4:b1 3:3
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79 4 5:b1 4:4
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80 5 6:a1 4:3
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81 6 7:a2 5:3
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82 ///
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83
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84 ENTRY G04183 Glycan
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85 COMPOSITION (Gal)3 (GlcNAc)5 (LFuc)1 (Man)3 (Neu5Ac)3
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86 MASS 3026.8
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87 CLASS Glycoprotein; N-Glycan
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88 DBLINKS CCSD: 41981
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89 GlycomeDB: 19974
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90 JCGGDB: JCGG-STR010756
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91 NODE 15
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92 1 GlcNAc 0 0
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93 2 GlcNAc -10 0
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94 3 Man -20 0
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95 4 Man -30 10
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96 5 Man -30 -10
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97 6 GlcNAc -40 10
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98 7 GlcNAc -40 -5
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99 8 GlcNAc -40 -15
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100 9 Gal -50 10
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101 10 Gal -50 0
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102 11 LFuc -50 -10
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103 12 Gal -50 -15
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104 13 Neu5Ac -60 10
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105 14 Neu5Ac -60 0
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106 15 Neu5Ac -60 -15
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107 EDGE 14
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108 1 2:b1 1:4
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109 2 3:b1 2:4
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110 3 4:a1 3:6
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111 4 5:a1 3:3
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112 5 6:b1 4:2
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113 6 7:b1 5:4
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114 7 8:b1 5:2
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115 8 9:b1 6:4
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116 9 10:b1 7:4
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117 10 11:a1 7:3
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118 11 12:b1 8:4
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119 12 13:a2 9:6
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120 13 14:a2 10:3
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121 14 15:a2 12:6
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122 ///
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123
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124 ENTRY G04329 Glycan
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125 COMPOSITION (Gal)3 (GlcNAc)3 (LFuc)3 (Neu5Ac)1
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126 MASS 1843.7
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127 DBLINKS CCSD: 36620
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128 GlycomeDB: 20084
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129 JCGGDB: JCGG-STR010874
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130 NODE 10
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131 1 GlcNAc 27 -5
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132 2 Gal 18 0
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133 3 LFuc 18 -10
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134 4 GlcNAc 9 0
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135 5 Gal 0 5
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136 6 LFuc 0 -5
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137 7 GlcNAc -9 5
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138 8 Gal -18 10
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139 9 LFuc -18 0
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140 10 Neu5Ac -27 10
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141 EDGE 9
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142 1 2:b1 1:4
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143 2 3:a1 1:3
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144 3 4:b1 2:3
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145 4 5:b1 4:4
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146 5 6:a1 4:3
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147 6 7:b1 5:3
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148 7 8:b1 7:4
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149 8 9:a1 7:3
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150 9 10:a2 8:3
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151 ///
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152 ENTRY G04804 Glycan
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153 COMPOSITION (Gal)3 (GlcNAc)5 (LFuc)1 (Man)3 (Neu5Ac)3
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154 MASS 3026.8
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155 CLASS Glycoprotein; N-Glycan
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156 REFERENCE 1 [PMID:6704968]
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157 Chandrasekaran EV, Davila M, Nixon D, Mendicino J.
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158 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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159 Cancer. Res. 44 (1984) 1557-67.
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160 DBLINKS CCSD: 8168
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161 GlycomeDB: 33225
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162 JCGGDB: JCGG-STR024138
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163 NODE 15
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164 1 GlcNAc 27.2 1.6
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165 2 GlcNAc 17.2 1.6
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166 3 Man 8.2 1.6
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167 4 Man 0.2 7.6
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168 5 Man 0.2 -4.4
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169 6 GlcNAc -8.8 7.6
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170 7 GlcNAc -8.8 -0.4
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171 8 GlcNAc -8.8 -8.4
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172 9 Gal -17.8 7.6
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173 10 Gal -17.8 3.6
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174 11 LFuc -17.8 -4.4
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175 12 Gal -17.8 -8.4
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176 13 Neu5Ac -26.8 7.6
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177 14 Neu5Ac -26.8 3.6
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178 15 Neu5Ac -26.8 -8.4
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179 EDGE 14
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180 1 2:b1 1:4
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181 2 3:b1 2:4
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182 3 4:a1 3:6
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183 4 5:a1 3:3
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184 5 6:b1 4:2
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185 6 7:b1 5:4
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186 7 8:b1 5:2
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187 8 9:b1 6:4
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188 9 10:b1 7:4
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189 10 11:a1 7:3
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190 11 12:b1 8:4
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191 12 13:a2 9:3
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192 13 14:a2 10:3
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193 14 15:a2 12:6
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194 ///
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195 """, "ringsmcaw_modified": """ENTRY G04845 Glycan
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196 NODE 9
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197 1 Glc 0 0
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198 2 Gal -10 0
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199 3 GlcNAc -20 10
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200 4 GlcNAc -20 -10
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201 5 Gal -30 15
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202 6 LFuc -30 5
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203 7 LFuc -30 -5
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204 8 Gal -30 -15
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205 9 Neu5Ac -40 15
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206 EDGE 8
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207 1 2:b1 1:4
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208 2 3:b1 2:6
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209 3 4:b1 2:3
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210 4 5:b1 3:4
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211 5 6:a1 3:3
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212 6 7:a1 4:4
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213 7 8:b1 4:3
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214 8 9:a2 5:3
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215 ///
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216 ENTRY G05108 Glycan
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217 NODE 7
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218 1 GalNAc 20 1
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219 2 Gal 10 1
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220 3 GlcNAc 0 1
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221 4 S -5 5
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222 5 Gal -10 1
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223 6 LFuc -10 -4
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224 7 Neu5Ac -20 1
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225 EDGE 6
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226 1 2:b1 1:3
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227 2 3:b1 2:3
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228 3 4 3:6
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229 4 5:b1 3:4
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230 5 6:a1 3:3
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231 6 7:a2 5:3
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232 ///
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233 ENTRY G05121 Glycan
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234 NODE 7
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235 1 GalNAc 0 0
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236 2 Neu5Ac -10 5
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237 3 Gal -10 -5
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238 4 GlcNAc -20 -5
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239 5 Gal -30 0
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240 6 LFuc -30 -10
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241 7 Neu5Ac -40 0
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242 EDGE 6
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243 1 2:a2 1:6
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244 2 3:b1 1:3
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245 3 4:b1 3:3
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246 4 5:b1 4:4
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247 5 6:a1 4:3
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248 6 7:a2 5:3
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249 ///
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250 ENTRY G04183 Glycan
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251 NODE 15
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252 1 GlcNAc 0 0
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253 2 GlcNAc -10 0
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254 3 Man -20 0
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255 4 Man -30 10
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256 5 Man -30 -10
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257 6 GlcNAc -40 10
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258 7 GlcNAc -40 -5
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259 8 GlcNAc -40 -15
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260 9 Gal -50 10
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261 10 Gal -50 0
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262 11 LFuc -50 -10
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263 12 Gal -50 -15
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264 13 Neu5Ac -60 10
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265 14 Neu5Ac -60 0
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266 15 Neu5Ac -60 -15
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267 EDGE 14
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268 1 2:b1 1:4
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269 2 3:b1 2:4
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270 3 4:a1 3:6
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271 4 5:a1 3:3
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272 5 6:b1 4:2
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273 6 7:b1 5:4
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274 7 8:b1 5:2
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275 8 9:b1 6:4
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276 9 10:b1 7:4
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277 10 11:a1 7:3
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278 11 12:b1 8:4
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279 12 13:a2 9:6
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280 13 14:a2 10:3
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281 14 15:a2 12:6
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282 ///
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283 ENTRY G04329 Glycan
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284 NODE 10
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285 1 GlcNAc 27 -5
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286 2 Gal 18 0
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287 3 LFuc 18 -10
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288 4 GlcNAc 9 0
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289 5 Gal 0 5
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290 6 LFuc 0 -5
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291 7 GlcNAc -9 5
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292 8 Gal -18 10
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293 9 LFuc -18 0
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294 10 Neu5Ac -27 10
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295 EDGE 9
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296 1 2:b1 1:4
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297 2 3:a1 1:3
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298 3 4:b1 2:3
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299 4 5:b1 4:4
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300 5 6:a1 4:3
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301 6 7:b1 5:3
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302 7 8:b1 7:4
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303 8 9:a1 7:3
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304 9 10:a2 8:3
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305 ///
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306 ENTRY G04804 Glycan
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307 NODE 15
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308 1 GlcNAc 27.2 1.6
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309 2 GlcNAc 17.2 1.6
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310 3 Man 8.2 1.6
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311 4 Man 0.2 7.6
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312 5 Man 0.2 -4.4
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313 6 GlcNAc -8.8 7.6
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314 7 GlcNAc -8.8 -0.4
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315 8 GlcNAc -8.8 -8.4
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316 9 Gal -17.8 7.6
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317 10 Gal -17.8 3.6
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318 11 LFuc -17.8 -4.4
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319 12 Gal -17.8 -8.4
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320 13 Neu5Ac -26.8 7.6
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321 14 Neu5Ac -26.8 3.6
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322 15 Neu5Ac -26.8 -8.4
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323 EDGE 14
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324 1 2:b1 1:4
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325 2 3:b1 2:4
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326 3 4:a1 3:6
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327 4 5:a1 3:3
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328 5 6:b1 4:2
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329 6 7:b1 5:4
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330 7 8:b1 5:2
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331 8 9:b1 6:4
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332 9 10:b1 7:4
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333 10 11:a1 7:3
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334 11 12:b1 8:4
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335 12 13:a2 9:3
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336 13 14:a2 10:3
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337 14 15:a2 12:6
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338 ///
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339 """, "ringsfinger": """ENTRY G00015 Glycan
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340 NODE 8
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341 1 Asn 20 0
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342 2 GlcNAc 12 0
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343 3 GlcNAc 3 0
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344 4 Man -5 0
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345 5 Man -12 5
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346 6 Man -12 -5
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347 7 GlcNAc -20 5
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348 8 GlcNAc -20 -5
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349 EDGE 7
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350 1 2:b1 1
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351 2 3:b1 2:4
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352 3 4:b1 3:4
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353 4 5:a1 4:6
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354 5 6:a1 4:3
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355 6 7:b1 5:2
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356 7 8:b1 6:2
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357 ///
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358 ENTRY G00016 Glycan
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359 NODE 9
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360 1 Asn 20 3
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361 2 GlcNAc 12 3
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362 3 LFuc 4 8
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363 4 GlcNAc 3 -2
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364 5 Man -5 -2
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365 6 Man -12 3
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366 7 Man -12 -7
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367 8 GlcNAc -20 3
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368 9 GlcNAc -20 -7
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369 EDGE 8
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370 1 2:b1 1
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371 2 3:a1 2:6
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372 3 4:b1 2:4
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373 4 5:b1 4:4
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374 5 6:a1 5:6
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375 6 7:a1 5:3
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376 7 8:b1 6:2
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377 8 9:b1 7:2
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378 ///
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379 ENTRY G00017 Glycan
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380 NODE 11
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381 1 Asn 24 3
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382 2 GlcNAc 14 3
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383 3 LFuc 7 8
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384 4 GlcNAc 6 -2
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385 5 Man -2 -2
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386 6 Man -8 3
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387 7 Man -8 -7
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388 8 GlcNAc -16 3
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389 9 GlcNAc -16 -7
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390 10 Gal -24 3
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391 11 Gal -24 -7
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392 EDGE 10
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393 1 2:b1 1
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394 2 3:a1 2:6
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395 3 4:b1 2:4
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396 4 5:b1 4:4
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397 5 6:a1 5:6
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398 6 7:a1 5:3
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399 7 8:b1 6:2
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400 8 9:b1 7:2
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401 9 10:b1 8:4
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402 10 11:b1 9:4
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403 ///
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404 ENTRY G00018 Glycan
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405 NODE 13
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406 1 Asn 28 3
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407 2 GlcNAc 18 3
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408 3 LFuc 10 8
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409 4 GlcNAc 9 -2
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410 5 Man 1 -2
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411 6 Man -5 4
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412 7 Man -5 -8
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413 8 GlcNAc -13 4
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414 9 GlcNAc -13 -8
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415 10 Gal -21 4
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416 11 Gal -21 -8
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417 12 Neu5Ac -29 4
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418 13 Neu5Ac -29 -8
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419 EDGE 12
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420 1 2:b1 1
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421 2 3:a1 2:6
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422 3 4:b1 2:4
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423 4 5:b1 4:4
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|
424 5 6:a1 5:6
|
|
|
425 6 7:a1 5:3
|
|
|
426 7 8:b1 6:2
|
|
|
427 8 9:b1 7:2
|
|
|
428 9 10:b1 8:4
|
|
|
429 10 11:b1 9:4
|
|
|
430 11 12:a2 10:6
|
|
|
431 12 13:a2 11:6
|
|
|
432 ///
|
|
|
433 ENTRY G00019 Glycan
|
|
|
434 NODE 9
|
|
|
435 1 Asn 20 0
|
|
|
436 2 GlcNAc 12 0
|
|
|
437 3 GlcNAc 3 0
|
|
|
438 4 Man -5 0
|
|
|
439 5 Man -12 5
|
|
|
440 6 Man -12 -5
|
|
|
441 7 GlcNAc -15 0
|
|
|
442 8 GlcNAc -20 5
|
|
|
443 9 GlcNAc -20 -5
|
|
|
444 EDGE 8
|
|
|
445 1 2:b1 1
|
|
|
446 2 3:b1 2:4
|
|
|
447 3 4:b1 3:4
|
|
|
448 4 5:a1 4:6
|
|
|
449 5 6:a1 4:3
|
|
|
450 6 7:b1 4:4
|
|
|
451 7 8:b1 5:2
|
|
|
452 8 9:b1 6:2
|
|
|
453 ///
|
|
|
454 ENTRY G00020 Glycan
|
|
|
455 NODE 9
|
|
|
456 1 Asn 20 3
|
|
|
457 2 GlcNAc 11 3
|
|
|
458 3 GlcNAc 2 3
|
|
|
459 4 Man -6 3
|
|
|
460 5 Man -13 9
|
|
|
461 6 Man -13 -3
|
|
|
462 7 GlcNAc -21 9
|
|
|
463 8 GlcNAc -21 2
|
|
|
464 9 GlcNAc -21 -8
|
|
|
465 EDGE 8
|
|
|
466 1 2:b1 1
|
|
|
467 2 3:b1 2:4
|
|
|
468 3 4:b1 3:4
|
|
|
469 4 5:a1 4:6
|
|
|
470 5 6:a1 4:3
|
|
|
471 6 7:b1 5:2
|
|
|
472 7 8:b1 6:4
|
|
|
473 8 9:b1 6:2
|
|
|
474 ///
|
|
|
475 """, "ringsbroken": """ABCDEFGENTRY G00015 Glycan
|
|
|
476 NODE 8
|
|
|
477 1 Asn 20 0
|
|
|
478 2 GlcNAc 12 0
|
|
|
479 """
|
|
|
480 }
|
|
|
481
|
|
|
482 self.kcoutput={"ringsmcaw":"""ENTRY G04845 Glycan
|
|
|
483 NODE 9
|
|
|
484 1 Glc 0 0
|
|
|
485 2 Gal -10 0
|
|
|
486 3 GlcNAc -20 10
|
|
|
487 4 GlcNAc -20 -10
|
|
|
488 5 Gal -30 15
|
|
|
489 6 LFuc -30 5
|
|
|
490 7 LFuc -30 -5
|
|
|
491 8 Gal -30 -15
|
|
|
492 9 Neu5Ac -40 15
|
|
|
493 EDGE 8
|
|
|
494 1 2:b1 1:4
|
|
|
495 2 3:b1 2:6
|
|
|
496 3 4:b1 2:3
|
|
|
497 4 5:b1 3:4
|
|
|
498 5 6:a1 3:3
|
|
|
499 6 7:a1 4:4
|
|
|
500 7 8:b1 4:3
|
|
|
501 8 9:a2 5:3
|
|
|
502 ///
|
|
|
503 ENTRY G05108 Glycan
|
|
|
504 NODE 7
|
|
|
505 1 GalNAc 20 1
|
|
|
506 2 Gal 10 1
|
|
|
507 3 GlcNAc 0 1
|
|
|
508 4 S -5 5
|
|
|
509 5 Gal -10 1
|
|
|
510 6 LFuc -10 -4
|
|
|
511 7 Neu5Ac -20 1
|
|
|
512 EDGE 6
|
|
|
513 1 2:b1 1:3
|
|
|
514 2 3:b1 2:3
|
|
|
515 3 4 3:6
|
|
|
516 4 5:b1 3:4
|
|
|
517 5 6:a1 3:3
|
|
|
518 6 7:a2 5:3
|
|
|
519 ///
|
|
|
520 ENTRY G05121 Glycan
|
|
|
521 NODE 7
|
|
|
522 1 GalNAc 0 0
|
|
|
523 2 Neu5Ac -10 5
|
|
|
524 3 Gal -10 -5
|
|
|
525 4 GlcNAc -20 -5
|
|
|
526 5 Gal -30 0
|
|
|
527 6 LFuc -30 -10
|
|
|
528 7 Neu5Ac -40 0
|
|
|
529 EDGE 6
|
|
|
530 1 2:a2 1:6
|
|
|
531 2 3:b1 1:3
|
|
|
532 3 4:b1 3:3
|
|
|
533 4 5:b1 4:4
|
|
|
534 5 6:a1 4:3
|
|
|
535 6 7:a2 5:3
|
|
|
536 ///
|
|
|
537 ENTRY G04183 Glycan
|
|
|
538 NODE 15
|
|
|
539 1 GlcNAc 0 0
|
|
|
540 2 GlcNAc -10 0
|
|
|
541 3 Man -20 0
|
|
|
542 4 Man -30 10
|
|
|
543 5 Man -30 -10
|
|
|
544 6 GlcNAc -40 10
|
|
|
545 7 GlcNAc -40 -5
|
|
|
546 8 GlcNAc -40 -15
|
|
|
547 9 Gal -50 10
|
|
|
548 10 Gal -50 0
|
|
|
549 11 LFuc -50 -10
|
|
|
550 12 Gal -50 -15
|
|
|
551 13 Neu5Ac -60 10
|
|
|
552 14 Neu5Ac -60 0
|
|
|
553 15 Neu5Ac -60 -15
|
|
|
554 EDGE 14
|
|
|
555 1 2:b1 1:4
|
|
|
556 2 3:b1 2:4
|
|
|
557 3 4:a1 3:6
|
|
|
558 4 5:a1 3:3
|
|
|
559 5 6:b1 4:2
|
|
|
560 6 7:b1 5:4
|
|
|
561 7 8:b1 5:2
|
|
|
562 8 9:b1 6:4
|
|
|
563 9 10:b1 7:4
|
|
|
564 10 11:a1 7:3
|
|
|
565 11 12:b1 8:4
|
|
|
566 12 13:a2 9:6
|
|
|
567 13 14:a2 10:3
|
|
|
568 14 15:a2 12:6
|
|
|
569 ///
|
|
|
570 ENTRY G04329 Glycan
|
|
|
571 NODE 10
|
|
|
572 1 GlcNAc 27 -5
|
|
|
573 2 Gal 18 0
|
|
|
574 3 LFuc 18 -10
|
|
|
575 4 GlcNAc 9 0
|
|
|
576 5 Gal 0 5
|
|
|
577 6 LFuc 0 -5
|
|
|
578 7 GlcNAc -9 5
|
|
|
579 8 Gal -18 10
|
|
|
580 9 LFuc -18 0
|
|
|
581 10 Neu5Ac -27 10
|
|
|
582 EDGE 9
|
|
|
583 1 2:b1 1:4
|
|
|
584 2 3:a1 1:3
|
|
|
585 3 4:b1 2:3
|
|
|
586 4 5:b1 4:4
|
|
|
587 5 6:a1 4:3
|
|
|
588 6 7:b1 5:3
|
|
|
589 7 8:b1 7:4
|
|
|
590 8 9:a1 7:3
|
|
|
591 9 10:a2 8:3
|
|
|
592 ///
|
|
|
593 ENTRY G04804 Glycan
|
|
|
594 NODE 15
|
|
|
595 1 GlcNAc 27.2 1.6
|
|
|
596 2 GlcNAc 17.2 1.6
|
|
|
597 3 Man 8.2 1.6
|
|
|
598 4 Man 0.2 7.6
|
|
|
599 5 Man 0.2 -4.4
|
|
|
600 6 GlcNAc -8.8 7.6
|
|
|
601 7 GlcNAc -8.8 -0.4
|
|
|
602 8 GlcNAc -8.8 -8.4
|
|
|
603 9 Gal -17.8 7.6
|
|
|
604 10 Gal -17.8 3.6
|
|
|
605 11 LFuc -17.8 -4.4
|
|
|
606 12 Gal -17.8 -8.4
|
|
|
607 13 Neu5Ac -26.8 7.6
|
|
|
608 14 Neu5Ac -26.8 3.6
|
|
|
609 15 Neu5Ac -26.8 -8.4
|
|
|
610 EDGE 14
|
|
|
611 1 2:b1 1:4
|
|
|
612 2 3:b1 2:4
|
|
|
613 3 4:a1 3:6
|
|
|
614 4 5:a1 3:3
|
|
|
615 5 6:b1 4:2
|
|
|
616 6 7:b1 5:4
|
|
|
617 7 8:b1 5:2
|
|
|
618 8 9:b1 6:4
|
|
|
619 9 10:b1 7:4
|
|
|
620 10 11:a1 7:3
|
|
|
621 11 12:b1 8:4
|
|
|
622 12 13:a2 9:3
|
|
|
623 13 14:a2 10:3
|
|
|
624 14 15:a2 12:6
|
|
|
625 ///
|
|
|
626 """}
|
|
|
627 os.environ["http_proxy"] = "" # work around for IOError: [Errno url error] invalid proxy for http:
|
|
|
628 pass
|
|
|
629
|
|
|
630 def tearDown(self):
|
|
|
631 pass
|
|
|
632
|
|
|
633 def test_simple_kcf(self):
|
|
|
634 import StringIO
|
|
|
635
|
|
|
636 kcinput = """ENTRY X Glycan
|
|
|
637 NODE 2
|
|
|
638 1 galnac 0 0
|
|
|
639 2 gal -8 0
|
|
|
640 EDGE 1
|
|
|
641 1 2:1 1
|
|
|
642 ///
|
|
|
643 """
|
|
|
644
|
|
|
645 kchandle = StringIO.StringIO(''.join(kcinput))
|
|
|
646 h = mk.read_meta_kcf(kchandle)
|
|
|
647 i = mk.flatten_meta_kcf_list(h)
|
|
|
648 self.assertIn("ENTRY X Glycan\n", i)
|
|
|
649 self.assertIn("NODE 2\n", i)
|
|
|
650 self.assertIn(" 1 2:1 1\n", i)
|
|
|
651
|
|
|
652
|
|
|
653
|
|
|
654 def test_multiple_kcf(self):
|
|
|
655 import StringIO
|
|
|
656
|
|
|
657 kcinput = """ENTRY ((A??)AN) Glycan
|
|
|
658 NODE 2
|
|
|
659 1 galnac 0 0
|
|
|
660 2 gal -8 0
|
|
|
661 EDGE 1
|
|
|
662 1 2:1 1
|
|
|
663 ///
|
|
|
664 ENTRY G00005 Glycan
|
|
|
665 NODE 6
|
|
|
666 1 PP-Dol 15 1
|
|
|
667 2 GlcNAc 8 1
|
|
|
668 3 GlcNAc 0 1
|
|
|
669 4 Man -9 1
|
|
|
670 5 Man -16 7
|
|
|
671 6 Man -16 -6
|
|
|
672 EDGE 5
|
|
|
673 1 2:a1 1
|
|
|
674 2 3:b1 2:4
|
|
|
675 3 4:b1 3:4
|
|
|
676 4 5:a1 4:6
|
|
|
677 5 6:a1 4:3
|
|
|
678 ///
|
|
|
679 """
|
|
|
680 kchandle = StringIO.StringIO(''.join(kcinput))
|
|
|
681 h = mk.read_meta_kcf(kchandle)
|
|
|
682 i = mk.flatten_meta_kcf_list(h)
|
|
|
683 self.assertIn(" 1 2:1 1\n", i)
|
|
|
684 self.assertIn(" 5 6:a1 4:3\n", i)
|
|
|
685
|
|
|
686 def test_empty_stream(self):
|
|
|
687 with self.assertRaises(IOError):
|
|
|
688 m = mk.read_meta_kcf(None)
|
|
|
689 with self.assertRaises(IOError):
|
|
|
690 m = mk.read_meta_kcf([])
|
|
|
691 with self.assertRaises(IOError):
|
|
|
692 m = mk.read_meta_kcf("")
|
|
|
693
|
|
|
694 def test_mcaw_kcf(self):
|
|
|
695 import StringIO
|
|
|
696 kcf = self.kcinput["ringsmcaw"]
|
|
|
697 handle = StringIO.StringIO(''.join(kcf))
|
|
|
698 h = mk.read_meta_kcf(handle)
|
|
|
699 i = mk.flatten_meta_kcf_list(h)
|
|
|
700 self.assertEqual(i,self.kcoutput["ringsmcaw"])
|
|
|
701
|
|
|
702 def run_tests():
|
|
|
703 unittest.main()
|
|
|
704
|
|
|
705
|
|
|
706 if __name__ == '__main__':
|
|
|
707 run_tests()
|
|
|
708
|
|
|
709
|
