Mercurial > repos > yufei-luo > s_mart
comparison commons/tools/tests/Test_F_MergeMatchsFiles.py @ 18:94ab73e8a190
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| author | m-zytnicki |
|---|---|
| date | Mon, 29 Apr 2013 03:20:15 -0400 |
| parents | |
| children |
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| 17:b0e8584489e6 | 18:94ab73e8a190 |
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| 1 import os | |
| 2 import unittest | |
| 3 from commons.core.utils.FileUtils import FileUtils | |
| 4 from commons.tools.MergeMatchsFiles import MergeMatchsFiles | |
| 5 | |
| 6 | |
| 7 class Test_F_MergeMatchsFiles(unittest.TestCase): | |
| 8 | |
| 9 def test_run_set(self): | |
| 10 inFileName1 = "test1.set" | |
| 11 inFileName2 = "test2.set" | |
| 12 self._writeSetFiles(inFileName1, inFileName2) | |
| 13 iMMF = MergeMatchsFiles("set", "out") | |
| 14 iMMF.run() | |
| 15 obsFileName = "out.set" | |
| 16 expFileName = "exp.set" | |
| 17 self._writeExpSetFile(expFileName) | |
| 18 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName)) | |
| 19 os.remove(expFileName) | |
| 20 os.remove(obsFileName) | |
| 21 | |
| 22 def test_run_align(self): | |
| 23 inFileName1 = "test1.align" | |
| 24 inFileName2 = "test2.align" | |
| 25 self._writeAlignFiles(inFileName1, inFileName2) | |
| 26 iMMF = MergeMatchsFiles("align", "out") | |
| 27 iMMF.run() | |
| 28 obsFileName = "out.align" | |
| 29 expFileName = "exp.align" | |
| 30 self._writeExpAlignFile(expFileName) | |
| 31 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName)) | |
| 32 os.remove(expFileName) | |
| 33 os.remove(obsFileName) | |
| 34 | |
| 35 def test_run_align_allByAll(self): | |
| 36 inFileName1 = "test1.align" | |
| 37 inFileName2 = "test2.align" | |
| 38 self._writeAlignFiles(inFileName1, inFileName2) | |
| 39 iMMF = MergeMatchsFiles("align", "out", True) | |
| 40 iMMF.run() | |
| 41 obsFileName = "out.align" | |
| 42 expFileName = "exp.align" | |
| 43 self._writeExpAlignFile_allByAll(expFileName) | |
| 44 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName)) | |
| 45 os.remove(expFileName) | |
| 46 os.remove(obsFileName) | |
| 47 | |
| 48 def test_run_path(self): | |
| 49 inFileName1 = "test1.path" | |
| 50 inFileName2 = "test2.path" | |
| 51 self._writePathFiles(inFileName1, inFileName2) | |
| 52 iMMF = MergeMatchsFiles("path", "out") | |
| 53 iMMF.run() | |
| 54 obsFileName = "out.path" | |
| 55 expFileName = "exp.path" | |
| 56 self._writeExpPathFile(expFileName) | |
| 57 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName)) | |
| 58 os.remove(expFileName) | |
| 59 os.remove(obsFileName) | |
| 60 | |
| 61 def test_run_tab(self): | |
| 62 inFileName1 = "test1.tab" | |
| 63 inFileName2 = "test2.tab" | |
| 64 self._writeTabFiles(inFileName1, inFileName2) | |
| 65 iMMF = MergeMatchsFiles("tab", "out") | |
| 66 iMMF.run() | |
| 67 obsFileName = "out.tab" | |
| 68 expFileName = "exp.tab" | |
| 69 self._writeExpTabFile(expFileName) | |
| 70 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName)) | |
| 71 os.remove(expFileName) | |
| 72 os.remove(obsFileName) | |
| 73 | |
| 74 def _writeSetFiles(self, fileName1, fileName2): | |
| 75 f = open(fileName1, "w") | |
| 76 f.write("1\t(TCTAT)3\tchunk006\t295\t309\n") | |
| 77 f.write("2\t(A)33\tchunk006\t679\t711\n") | |
| 78 f.write("3\t(G)16\tchunk006\t731\t746\n") | |
| 79 f.write("4\t(GAG)9\tchunk006\t903\t929\n") | |
| 80 f.write("5\t(GGAGGG)4\tchunk006\t905\t929\n") | |
| 81 f.close() | |
| 82 f = open(fileName2, "w") | |
| 83 f.write("1\t(CCACT)3\tchunk011\t101\t116\n") | |
| 84 f.write("2\t(TATATA)7\tchunk011\t316\t357\n") | |
| 85 f.write("3\t(AT)22\tchunk011\t323\t366\n") | |
| 86 f.close() | |
| 87 | |
| 88 def _writeExpSetFile(self, fileName): | |
| 89 f = open(fileName, "w") | |
| 90 f.write("1\t(TCTAT)3\tchunk006\t295\t309\n") | |
| 91 f.write("2\t(A)33\tchunk006\t679\t711\n") | |
| 92 f.write("3\t(G)16\tchunk006\t731\t746\n") | |
| 93 f.write("4\t(GAG)9\tchunk006\t903\t929\n") | |
| 94 f.write("5\t(GGAGGG)4\tchunk006\t905\t929\n") | |
| 95 f.write("6\t(CCACT)3\tchunk011\t101\t116\n") | |
| 96 f.write("7\t(TATATA)7\tchunk011\t316\t357\n") | |
| 97 f.write("8\t(AT)22\tchunk011\t323\t366\n") | |
| 98 f.close() | |
| 99 | |
| 100 def _writeAlignFiles(self, fileName1, fileName2): | |
| 101 f = open(fileName1, "w") | |
| 102 f.write("chunk1\t25601\t27800\tchunk1\t52250\t54450\t0\t4244\t99.36\n") | |
| 103 f.write("chunk1\t27791\t28620\tchunk1\t55918\t56749\t0\t1588\t99.16\n") | |
| 104 f.write("chunk1\t28618\t32380\tchunk1\t56794\t60572\t0\t7299\t99.29\n") | |
| 105 f.write("chunk1\t28692\t30872\tchunk1\t49901\t52081\t0\t4260\t99.63\n") | |
| 106 f.write("chunk1\t32216\t34275\tchunk1\t52084\t54143\t0\t4012\t99.56\n") | |
| 107 f.write("chunk1\t41016\t45652\tchunk1\t55918\t60572\t0\t8942\t99.18\n") | |
| 108 f.write("chunk1\t41964\t44144\tchunk1\t49901\t52081\t0\t4252\t99.59\n") | |
| 109 f.write("chunk1\t46237\t46863\tchunk1\t73980\t74625\t0\t837\t91.36\n") | |
| 110 f.write("chunk1\t46330\t46860\tchunk1\t54981\t54450\t0\t841\t95.11\n") | |
| 111 f.write("chunk1\t46861\t48962\tchunk1\t52349\t54450\t0\t4103\t99.62\n") | |
| 112 f.write("chunk1\t48953\t50000\tchunk1\t55918\t56967\t0\t2036\t99.52\n") | |
| 113 f.write("chunk1\t49901\t52081\tchunk1\t28692\t30872\t0\t4260\t99.63\n") | |
| 114 f.write("chunk1\t49901\t52081\tchunk1\t41964\t44144\t0\t4252\t99.59\n") | |
| 115 f.write("chunk1\t52084\t54143\tchunk1\t32216\t34275\t0\t4012\t99.56\n") | |
| 116 f.write("chunk1\t52250\t54450\tchunk1\t25601\t27800\t0\t4244\t99.36\n") | |
| 117 f.write("chunk1\t52349\t54450\tchunk1\t46861\t48962\t0\t4103\t99.62\n") | |
| 118 f.write("chunk1\t54450\t54980\tchunk1\t74622\t74091\t0\t769\t93.63\n") | |
| 119 f.write("chunk1\t54450\t54981\tchunk1\t46860\t46330\t0\t841\t95.11\n") | |
| 120 f.write("chunk1\t55918\t56749\tchunk1\t27791\t28620\t0\t1588\t99.16\n") | |
| 121 f.write("chunk1\t55918\t56967\tchunk1\t48953\t50000\t0\t2036\t99.52\n") | |
| 122 f.write("chunk1\t55918\t60572\tchunk1\t41016\t45652\t0\t8942\t99.18\n") | |
| 123 f.write("chunk1\t56794\t60572\tchunk1\t28618\t32380\t0\t7299\t99.29\n") | |
| 124 f.write("chunk1\t73980\t74625\tchunk1\t46237\t46863\t0\t837\t91.36\n") | |
| 125 f.write("chunk1\t74091\t74622\tchunk1\t54980\t54450\t0\t769\t93.63\n") | |
| 126 f.write("chunk1\t99211\t99791\tchunk1\t164000\t164577\t0\t767\t91.74\n") | |
| 127 f.write("chunk1\t101527\t102429\tchunk1\t167161\t168059\t0\t1074\t90.14\n") | |
| 128 f.write("chunk1\t164000\t164577\tchunk1\t99211\t99791\t0\t767\t91.74\n") | |
| 129 f.write("chunk1\t167161\t168059\tchunk1\t101527\t102429\t0\t1074\t90.14\n") | |
| 130 f.write("chunk1\t46330\t46862\tchunk6\t2564\t3101\t0\t835\t94.8\n") | |
| 131 f.write("chunk1\t46372\t46862\tchunk6\t5328\t4837\t0\t753\t94.51\n") | |
| 132 f.write("chunk1\t54450\t54915\tchunk6\t4839\t5304\t0\t749\t95.28\n") | |
| 133 f.write("chunk1\t54450\t55021\tchunk6\t3099\t2524\t0\t878\t94.27\n") | |
| 134 f.write("chunk1\t54600\t55021\tchunk6\t25505\t25926\t0\t638\t94.08\n") | |
| 135 f.write("chunk1\t74091\t74624\tchunk6\t2565\t3101\t0\t898\t96.48\n") | |
| 136 f.write("chunk1\t74132\t74624\tchunk6\t5328\t4837\t0\t763\t94.95\n") | |
| 137 f.close() | |
| 138 f = open(fileName2, "w") | |
| 139 f.write("chunk6\t2524\t3099\tchunk1\t55021\t54450\t0\t878\t94.27\n") | |
| 140 f.write("chunk6\t2564\t3101\tchunk1\t46330\t46862\t0\t835\t94.8\n") | |
| 141 f.write("chunk6\t2565\t3101\tchunk1\t74091\t74624\t0\t898\t96.48\n") | |
| 142 f.write("chunk6\t4837\t5328\tchunk1\t46862\t46372\t0\t753\t94.51\n") | |
| 143 f.write("chunk6\t4837\t5328\tchunk1\t74624\t74132\t0\t763\t94.95\n") | |
| 144 f.write("chunk6\t4839\t5304\tchunk1\t54450\t54915\t0\t749\t95.28\n") | |
| 145 f.write("chunk6\t25505\t25926\tchunk1\t54600\t55021\t0\t638\t94.08\n") | |
| 146 f.write("chunk6\t1998\t2948\tchunk6\t26450\t25506\t0\t1758\t98.42\n") | |
| 147 f.write("chunk6\t2606\t3101\tchunk6\t5328\t4837\t0\t815\t95.77\n") | |
| 148 f.write("chunk6\t4837\t5328\tchunk6\t3101\t2606\t0\t815\t95.77\n") | |
| 149 f.write("chunk6\t25506\t26450\tchunk6\t2948\t1998\t0\t1758\t98.42\n") | |
| 150 f.write("chunk6\t95526\t96047\tchunk6\t115678\t116199\t0\t688\t92.19\n") | |
| 151 f.write("chunk6\t115678\t116199\tchunk6\t95526\t96047\t0\t688\t92.19\n") | |
| 152 f.close() | |
| 153 | |
| 154 def _writeExpAlignFile_allByAll(self, fileName): | |
| 155 f = open(fileName, "w") | |
| 156 f.write("chunk1\t25601\t27800\tchunk1\t52250\t54450\t0\t4244\t99.360000\n") | |
| 157 f.write("chunk1\t27791\t28620\tchunk1\t55918\t56749\t0\t1588\t99.160000\n") | |
| 158 f.write("chunk1\t28618\t32380\tchunk1\t56794\t60572\t0\t7299\t99.290000\n") | |
| 159 f.write("chunk1\t28692\t30872\tchunk1\t49901\t52081\t0\t4260\t99.630000\n") | |
| 160 f.write("chunk1\t32216\t34275\tchunk1\t52084\t54143\t0\t4012\t99.560000\n") | |
| 161 f.write("chunk1\t41016\t45652\tchunk1\t55918\t60572\t0\t8942\t99.180000\n") | |
| 162 f.write("chunk1\t41964\t44144\tchunk1\t49901\t52081\t0\t4252\t99.590000\n") | |
| 163 f.write("chunk1\t46237\t46863\tchunk1\t73980\t74625\t0\t837\t91.360000\n") | |
| 164 f.write("chunk1\t46330\t46860\tchunk1\t54981\t54450\t0\t841\t95.110000\n") | |
| 165 f.write("chunk1\t46861\t48962\tchunk1\t52349\t54450\t0\t4103\t99.620000\n") | |
| 166 f.write("chunk1\t48953\t50000\tchunk1\t55918\t56967\t0\t2036\t99.520000\n") | |
| 167 f.write("chunk1\t54450\t54980\tchunk1\t74622\t74091\t0\t769\t93.630000\n") | |
| 168 f.write("chunk1\t99211\t99791\tchunk1\t164000\t164577\t0\t767\t91.740000\n") | |
| 169 f.write("chunk1\t101527\t102429\tchunk1\t167161\t168059\t0\t1074\t90.140000\n") | |
| 170 f.write("chunk1\t46330\t46862\tchunk6\t2564\t3101\t0\t835\t94.800000\n") | |
| 171 f.write("chunk1\t46372\t46862\tchunk6\t5328\t4837\t0\t753\t94.510000\n") | |
| 172 f.write("chunk1\t54450\t54915\tchunk6\t4839\t5304\t0\t749\t95.280000\n") | |
| 173 f.write("chunk1\t54450\t55021\tchunk6\t3099\t2524\t0\t878\t94.270000\n") | |
| 174 f.write("chunk1\t54600\t55021\tchunk6\t25505\t25926\t0\t638\t94.080000\n") | |
| 175 f.write("chunk1\t74091\t74624\tchunk6\t2565\t3101\t0\t898\t96.480000\n") | |
| 176 f.write("chunk1\t74132\t74624\tchunk6\t5328\t4837\t0\t763\t94.950000\n") | |
| 177 f.write("chunk6\t1998\t2948\tchunk6\t26450\t25506\t0\t1758\t98.420000\n") | |
| 178 f.write("chunk6\t2606\t3101\tchunk6\t5328\t4837\t0\t815\t95.770000\n") | |
| 179 f.write("chunk6\t95526\t96047\tchunk6\t115678\t116199\t0\t688\t92.190000\n") | |
| 180 f.close() | |
| 181 | |
| 182 def _writeExpAlignFile(self, fileName): | |
| 183 f = open(fileName, "w") | |
| 184 f.write("chunk1\t25601\t27800\tchunk1\t52250\t54450\t0\t4244\t99.36\n") | |
| 185 f.write("chunk1\t27791\t28620\tchunk1\t55918\t56749\t0\t1588\t99.16\n") | |
| 186 f.write("chunk1\t28618\t32380\tchunk1\t56794\t60572\t0\t7299\t99.29\n") | |
| 187 f.write("chunk1\t28692\t30872\tchunk1\t49901\t52081\t0\t4260\t99.63\n") | |
| 188 f.write("chunk1\t32216\t34275\tchunk1\t52084\t54143\t0\t4012\t99.56\n") | |
| 189 f.write("chunk1\t41016\t45652\tchunk1\t55918\t60572\t0\t8942\t99.18\n") | |
| 190 f.write("chunk1\t41964\t44144\tchunk1\t49901\t52081\t0\t4252\t99.59\n") | |
| 191 f.write("chunk1\t46237\t46863\tchunk1\t73980\t74625\t0\t837\t91.36\n") | |
| 192 f.write("chunk1\t46330\t46860\tchunk1\t54981\t54450\t0\t841\t95.11\n") | |
| 193 f.write("chunk1\t46861\t48962\tchunk1\t52349\t54450\t0\t4103\t99.62\n") | |
| 194 f.write("chunk1\t48953\t50000\tchunk1\t55918\t56967\t0\t2036\t99.52\n") | |
| 195 f.write("chunk1\t49901\t52081\tchunk1\t28692\t30872\t0\t4260\t99.63\n") | |
| 196 f.write("chunk1\t49901\t52081\tchunk1\t41964\t44144\t0\t4252\t99.59\n") | |
| 197 f.write("chunk1\t52084\t54143\tchunk1\t32216\t34275\t0\t4012\t99.56\n") | |
| 198 f.write("chunk1\t52250\t54450\tchunk1\t25601\t27800\t0\t4244\t99.36\n") | |
| 199 f.write("chunk1\t52349\t54450\tchunk1\t46861\t48962\t0\t4103\t99.62\n") | |
| 200 f.write("chunk1\t54450\t54980\tchunk1\t74622\t74091\t0\t769\t93.63\n") | |
| 201 f.write("chunk1\t54450\t54981\tchunk1\t46860\t46330\t0\t841\t95.11\n") | |
| 202 f.write("chunk1\t55918\t56749\tchunk1\t27791\t28620\t0\t1588\t99.16\n") | |
| 203 f.write("chunk1\t55918\t56967\tchunk1\t48953\t50000\t0\t2036\t99.52\n") | |
| 204 f.write("chunk1\t55918\t60572\tchunk1\t41016\t45652\t0\t8942\t99.18\n") | |
| 205 f.write("chunk1\t56794\t60572\tchunk1\t28618\t32380\t0\t7299\t99.29\n") | |
| 206 f.write("chunk1\t73980\t74625\tchunk1\t46237\t46863\t0\t837\t91.36\n") | |
| 207 f.write("chunk1\t74091\t74622\tchunk1\t54980\t54450\t0\t769\t93.63\n") | |
| 208 f.write("chunk1\t99211\t99791\tchunk1\t164000\t164577\t0\t767\t91.74\n") | |
| 209 f.write("chunk1\t101527\t102429\tchunk1\t167161\t168059\t0\t1074\t90.14\n") | |
| 210 f.write("chunk1\t164000\t164577\tchunk1\t99211\t99791\t0\t767\t91.74\n") | |
| 211 f.write("chunk1\t167161\t168059\tchunk1\t101527\t102429\t0\t1074\t90.14\n") | |
| 212 f.write("chunk1\t46330\t46862\tchunk6\t2564\t3101\t0\t835\t94.8\n") | |
| 213 f.write("chunk1\t46372\t46862\tchunk6\t5328\t4837\t0\t753\t94.51\n") | |
| 214 f.write("chunk1\t54450\t54915\tchunk6\t4839\t5304\t0\t749\t95.28\n") | |
| 215 f.write("chunk1\t54450\t55021\tchunk6\t3099\t2524\t0\t878\t94.27\n") | |
| 216 f.write("chunk1\t54600\t55021\tchunk6\t25505\t25926\t0\t638\t94.08\n") | |
| 217 f.write("chunk1\t74091\t74624\tchunk6\t2565\t3101\t0\t898\t96.48\n") | |
| 218 f.write("chunk1\t74132\t74624\tchunk6\t5328\t4837\t0\t763\t94.95\n") | |
| 219 f.write("chunk6\t2524\t3099\tchunk1\t55021\t54450\t0\t878\t94.27\n") | |
| 220 f.write("chunk6\t2564\t3101\tchunk1\t46330\t46862\t0\t835\t94.8\n") | |
| 221 f.write("chunk6\t2565\t3101\tchunk1\t74091\t74624\t0\t898\t96.48\n") | |
| 222 f.write("chunk6\t4837\t5328\tchunk1\t46862\t46372\t0\t753\t94.51\n") | |
| 223 f.write("chunk6\t4837\t5328\tchunk1\t74624\t74132\t0\t763\t94.95\n") | |
| 224 f.write("chunk6\t4839\t5304\tchunk1\t54450\t54915\t0\t749\t95.28\n") | |
| 225 f.write("chunk6\t25505\t25926\tchunk1\t54600\t55021\t0\t638\t94.08\n") | |
| 226 f.write("chunk6\t1998\t2948\tchunk6\t26450\t25506\t0\t1758\t98.42\n") | |
| 227 f.write("chunk6\t2606\t3101\tchunk6\t5328\t4837\t0\t815\t95.77\n") | |
| 228 f.write("chunk6\t4837\t5328\tchunk6\t3101\t2606\t0\t815\t95.77\n") | |
| 229 f.write("chunk6\t25506\t26450\tchunk6\t2948\t1998\t0\t1758\t98.42\n") | |
| 230 f.write("chunk6\t95526\t96047\tchunk6\t115678\t116199\t0\t688\t92.19\n") | |
| 231 f.write("chunk6\t115678\t116199\tchunk6\t95526\t96047\t0\t688\t92.19\n") | |
| 232 f.close() | |
| 233 | |
| 234 def _writePathFiles(self, fileName1, fileName2): | |
| 235 f = open(fileName1, "w") | |
| 236 f.write("1\tchunk001\t11046\t11071\tAT_rich#Low_complexity\t166\t141\t0.0\t9\t34.62\n") | |
| 237 f.write("2\tchunk001\t11050\t11074\tAT_rich#Low_complexity\t161\t137\t0.0\t14\t56.0\n") | |
| 238 f.write("3\tchunk001\t17216\t17266\tAT_rich#Low_complexity\t144\t194\t0.0\t14\t29.41\n") | |
| 239 f.write("4\tchunk001\t17736\t17766\tAT_rich#Low_complexity\t118\t148\t0.0\t6\t22.58\n") | |
| 240 f.write("5\tchunk001\t18723\t18758\tAT_rich#Low_complexity\t110\t145\t0.0\t5\t13.89\n") | |
| 241 f.write("6\tchunk001\t20024\t20073\tAT_rich#Low_complexity\t125\t174\t0.0\t13\t26.0\n") | |
| 242 f.write("7\tchunk002\t12855\t12882\tAT_rich#Low_complexity\t131\t158\t0.0\t13\t46.43\n") | |
| 243 f.write("8\tchunk002\t20736\t20771\tAT_rich#Low_complexity\t135\t170\t0.0\t12\t36.11\n") | |
| 244 f.close() | |
| 245 f = open(fileName2, "w") | |
| 246 f.write("1\tchunk006\t12114\t12143\tAT_rich#Low_complexity\t146\t117\t0.0\t6\t20.0\n") | |
| 247 f.write("2\tchunk006\t25538\t25574\tAT_rich#Low_complexity\t128\t164\t0.0\t14\t37.84\n") | |
| 248 f.write("3\tchunk006\t25794\t25818\tAT_rich#Low_complexity\t162\t138\t0.0\t15\t60.0\n") | |
| 249 f.write("4\tchunk006\t28373\t28403\tAT_rich#Low_complexity\t135\t165\t0.0\t17\t54.84\n") | |
| 250 f.write("5\tchunk006\t29180\t29201\tAT_rich#Low_complexity\t163\t142\t0.0\t14\t68.18\n") | |
| 251 f.write("6\tchunk006\t33773\t33825\tAT_rich#Low_complexity\t142\t194\t0.0\t11\t22.64\n") | |
| 252 f.close() | |
| 253 | |
| 254 def _writeExpPathFile(self, fileName): | |
| 255 f = open(fileName, "w") | |
| 256 f.write("1\tchunk001\t11046\t11071\tAT_rich#Low_complexity\t166\t141\t0.0\t9\t34.62\n") | |
| 257 f.write("2\tchunk001\t11050\t11074\tAT_rich#Low_complexity\t161\t137\t0.0\t14\t56.0\n") | |
| 258 f.write("3\tchunk001\t17216\t17266\tAT_rich#Low_complexity\t144\t194\t0.0\t14\t29.41\n") | |
| 259 f.write("4\tchunk001\t17736\t17766\tAT_rich#Low_complexity\t118\t148\t0.0\t6\t22.58\n") | |
| 260 f.write("5\tchunk001\t18723\t18758\tAT_rich#Low_complexity\t110\t145\t0.0\t5\t13.89\n") | |
| 261 f.write("6\tchunk001\t20024\t20073\tAT_rich#Low_complexity\t125\t174\t0.0\t13\t26.0\n") | |
| 262 f.write("7\tchunk002\t12855\t12882\tAT_rich#Low_complexity\t131\t158\t0.0\t13\t46.43\n") | |
| 263 f.write("8\tchunk002\t20736\t20771\tAT_rich#Low_complexity\t135\t170\t0.0\t12\t36.11\n") | |
| 264 f.write("9\tchunk006\t12114\t12143\tAT_rich#Low_complexity\t146\t117\t0.0\t6\t20.0\n") | |
| 265 f.write("10\tchunk006\t25538\t25574\tAT_rich#Low_complexity\t128\t164\t0.0\t14\t37.84\n") | |
| 266 f.write("11\tchunk006\t25794\t25818\tAT_rich#Low_complexity\t162\t138\t0.0\t15\t60.0\n") | |
| 267 f.write("12\tchunk006\t28373\t28403\tAT_rich#Low_complexity\t135\t165\t0.0\t17\t54.84\n") | |
| 268 f.write("13\tchunk006\t29180\t29201\tAT_rich#Low_complexity\t163\t142\t0.0\t14\t68.18\n") | |
| 269 f.write("14\tchunk006\t33773\t33825\tAT_rich#Low_complexity\t142\t194\t0.0\t11\t22.64\n") | |
| 270 f.close() | |
| 271 | |
| 272 def _writeTabFiles(self, fileName1, fileName2): | |
| 273 f = open(fileName1, "w") | |
| 274 f.write("query.name\tquery.start\tquery.end\tquery.length\tquery.length.%\tmatch.length.%\tsubject.name\tsubject.start\tsubject.end\tsubject.length\tsubject.length.%\tE.value\tScore\tIdentity\tpath\n") | |
| 275 f.write("DmelChr4_bench_Blaster_Grouper_1_Map_3\t2\t542\t541\t0.998155\t0.32473\tTC1_DM:ClassII:TIR:Tc1-Mariner\t1\t543\t543\t0.32593\t1.4e-93\t984\t87.541\t1\n") | |
| 276 f.write("DmelChr4_bench_Blaster_Grouper_2_Map_8\t2\t517\t516\t0.998066\t0.115179\tPROTOP:ClassII:TIR:P\t530\t16\t515\t0.114955\t1.2e-79\t928\t95.2118\t2\n") | |
| 277 f.write("DmelChr4_bench_Blaster_Grouper_3_Map_20\t5\t598\t594\t0.978583\t0.537557\tPROTOP_A:ClassII:TIR:P\t572\t1\t572\t0.517647\t3e-93\t1048\t97.6307\t3\n") | |
| 278 f.write("DmelChr4_bench_Blaster_Grouper_4_Map_3\t5\t534\t530\t0.992509\t0.479638\tPROTOP_A:ClassII:TIR:P\t1105\t576\t530\t0.479638\t2.9e-87\t1828\t98.4848\t4\n") | |
| 279 f.write("DmelChr4_bench_Blaster_Grouper_5_Map_3\t5\t704\t700\t0.994318\t0.425791\tTC1-2_DM:ClassII:TIR:Tc1-Mariner\t1644\t945\t700\t0.425791\t7.3e-120\t1228\t98.1349\t5\n") | |
| 280 f.close() | |
| 281 f = open(fileName2, "w") | |
| 282 f.write("query.name\tquery.start\tquery.end\tquery.length\tquery.length.%\tmatch.length.%\tsubject.name\tsubject.start\tsubject.end\tsubject.length\tsubject.length.%\tE.value\tScore\tIdentity\tpath\n") | |
| 283 f.write("DmelChr4_bench_Blaster_Grouper_5_Map_3\t274\t702\t429\t0.609375\t1.26176\tTC1-2_DMp:ClassII:TIR:Tc1-Mariner\t340\t198\t143\t0.420588\t5e-74\t265\t98.6014\t1\n") | |
| 284 f.write("DmelChr4_bench_Blaster_Recon_12_Map_3\t311\t374\t64\t0.028021\t0.0359349\tBEL-27_AA-I_1p:ClassI:LTR:Bel-Pao\t605\t582\t24\t0.0134756\t6.3e-17\t11\t30.8511\t2\n") | |
| 285 f.write("DmelChr4_bench_Blaster_Recon_12_Map_3\t1472\t1552\t81\t0.0354641\t0.0463918\tBEL-76_AA-I_1p:ClassI:LTR:Bel-Pao\t79\t52\t28\t0.0160367\t1e-13\t8\t27.7778\t3\n") | |
| 286 f.close() | |
| 287 | |
| 288 def _writeExpTabFile(self, fileName): | |
| 289 f = open(fileName, "w") | |
| 290 f.write("query.name\tquery.start\tquery.end\tquery.length\tquery.length.%\tmatch.length.%\tsubject.name\tsubject.start\tsubject.end\tsubject.length\tsubject.length.%\tE.value\tScore\tIdentity\tpath\n") | |
| 291 f.write("DmelChr4_bench_Blaster_Grouper_1_Map_3\t2\t542\t541\t0.998155\t0.32473\tTC1_DM:ClassII:TIR:Tc1-Mariner\t1\t543\t543\t0.32593\t1.4e-93\t984\t87.541\t1\n") | |
| 292 f.write("DmelChr4_bench_Blaster_Grouper_2_Map_8\t2\t517\t516\t0.998066\t0.115179\tPROTOP:ClassII:TIR:P\t530\t16\t515\t0.114955\t1.2e-79\t928\t95.2118\t2\n") | |
| 293 f.write("DmelChr4_bench_Blaster_Grouper_3_Map_20\t5\t598\t594\t0.978583\t0.537557\tPROTOP_A:ClassII:TIR:P\t572\t1\t572\t0.517647\t3e-93\t1048\t97.6307\t3\n") | |
| 294 f.write("DmelChr4_bench_Blaster_Grouper_4_Map_3\t5\t534\t530\t0.992509\t0.479638\tPROTOP_A:ClassII:TIR:P\t1105\t576\t530\t0.479638\t2.9e-87\t1828\t98.4848\t4\n") | |
| 295 f.write("DmelChr4_bench_Blaster_Grouper_5_Map_3\t5\t704\t700\t0.994318\t0.425791\tTC1-2_DM:ClassII:TIR:Tc1-Mariner\t1644\t945\t700\t0.425791\t7.3e-120\t1228\t98.1349\t5\n") | |
| 296 f.write("DmelChr4_bench_Blaster_Grouper_5_Map_3\t274\t702\t429\t0.609375\t1.26176\tTC1-2_DMp:ClassII:TIR:Tc1-Mariner\t340\t198\t143\t0.420588\t5e-74\t265\t98.6014\t6\n") | |
| 297 f.write("DmelChr4_bench_Blaster_Recon_12_Map_3\t311\t374\t64\t0.028021\t0.0359349\tBEL-27_AA-I_1p:ClassI:LTR:Bel-Pao\t605\t582\t24\t0.0134756\t6.3e-17\t11\t30.8511\t7\n") | |
| 298 f.write("DmelChr4_bench_Blaster_Recon_12_Map_3\t1472\t1552\t81\t0.0354641\t0.0463918\tBEL-76_AA-I_1p:ClassI:LTR:Bel-Pao\t79\t52\t28\t0.0160367\t1e-13\t8\t27.7778\t8\n") | |
| 299 f.close() | |
| 300 | |
| 301 if __name__ == "__main__": | |
| 302 unittest.main() |