Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/SMART/Java/Python/ncList/test/Test_F_NCList.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author | yufei-luo |
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date | Thu, 17 Jan 2013 10:52:14 -0500 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 import os |
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2 import unittest |
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3 import struct |
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4 from SMART.Java.Python.ncList.NCList import NCList |
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5 from SMART.Java.Python.misc import Utils |
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6 from commons.core.utils.FileUtils import FileUtils |
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7 from SMART.Java.Python.ncList.test.MockFindOverlapsWithSeveralIntervals import * |
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8 from commons.core.parsing.GffParser import GffParser |
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9 from SMART.Java.Python.ncList.FileSorter import FileSorter |
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10 |
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11 class Test_F_NCList(unittest.TestCase): |
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12 |
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13 def setUp(self): |
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14 self._inputGff3FileName = 'sortedFile.gff3' |
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15 self._sortedFileName = 'sortedFile.pkl' |
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16 self._expHFileName = 'expH.bin' |
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17 self._expLFileName = 'expL.bin' |
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18 self._obsHFileName = 'H.bin' |
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19 self._obsLFileName = 'L.bin' |
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20 self._addressFileName = 'address.txt' |
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21 self._writeGFF3File(self._inputGff3FileName) |
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22 self._ncList = NCList(0) |
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23 self._ncList.setChromosome("chr1") |
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24 |
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25 def tearDown(self): |
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26 return |
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27 for fileName in (self._inputGff3FileName, self._sortedFileName, self._expHFileName, self._expLFileName, self._obsHFileName, self._obsLFileName, self._addressFileName): |
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28 if os.path.exists(fileName): |
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29 os.remove(fileName) |
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30 |
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31 def _sortAndBuild(self): |
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32 parser = GffParser(self._inputGff3FileName) |
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33 fs = FileSorter(parser, 0) |
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34 fs.setOutputFileName(self._sortedFileName) |
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35 fs.sort() |
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36 self._ncList.setFileName(self._sortedFileName) |
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37 self._ncList.setNbElements(parser.getNbTranscripts()) |
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38 self._ncList.buildLists() |
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39 |
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40 def test_run_with_one_elementSubList(self): |
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41 iMock = MockFindOverlapsWithOneInterval() |
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42 iMock.write(self._inputGff3FileName) |
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43 self._sortAndBuild() |
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44 self._writeExpHFile_one_elementSubList() |
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45 self._writeExpLFile_one_elementSubList() |
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46 self.assertTrue(FileUtils.are2FilesIdentical(self._expHFileName, self._ncList._hFileName)) |
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47 self.assertTrue(FileUtils.are2FilesIdentical(self._expLFileName, self._ncList._lFileName)) |
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48 |
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49 def test_case1(self): |
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50 iMock = MockFindOverlapsWithServeralIntervals_case1() |
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51 iMock.write(self._inputGff3FileName) |
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52 self._sortAndBuild() |
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53 self._writeExpHFileCase1() |
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54 self._writeExpLFileCase1() |
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55 self.assertTrue(FileUtils.are2FilesIdentical(self._expHFileName, self._ncList._hFileName)) |
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56 self.assertTrue(FileUtils.are2FilesIdentical(self._expLFileName, self._ncList._lFileName)) |
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57 |
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58 def test_case2(self): |
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59 iMock = MockFindOverlapsWithServeralIntervals_case2() |
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60 iMock.write(self._inputGff3FileName) |
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61 self._sortAndBuild() |
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62 self._writeExpHFileCase2() |
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63 self._writeExpLFileCase2() |
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64 self.assertTrue(FileUtils.are2FilesIdentical(self._expHFileName, self._ncList._hFileName)) |
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65 self.assertTrue(FileUtils.are2FilesIdentical(self._expLFileName, self._ncList._lFileName)) |
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66 |
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67 def test_case3(self): |
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68 iMock = MockFindOverlapsWithServeralIntervals_case3() |
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69 iMock.write(self._inputGff3FileName) |
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70 self._sortAndBuild() |
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71 self._writeExpHFileCase3() |
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72 self._writeExpLFileCase3() |
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73 self.assertTrue(FileUtils.are2FilesIdentical(self._expHFileName, self._ncList._hFileName)) |
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74 self.assertTrue(FileUtils.are2FilesIdentical(self._expLFileName, self._ncList._lFileName)) |
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75 |
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76 def test_case4_5(self): |
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77 iMock = MockFindOverlapsWithServeralIntervals_case4_5() |
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78 iMock.write(self._inputGff3FileName) |
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79 self._sortAndBuild() |
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80 self._writeExpHFileCase4_5() |
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81 self._writeExpLFileCase4_5() |
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82 self.assertTrue(FileUtils.are2FilesIdentical(self._expHFileName, self._ncList._hFileName)) |
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83 self.assertTrue(FileUtils.are2FilesIdentical(self._expLFileName, self._ncList._lFileName)) |
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84 |
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85 def test_case6_7(self): |
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86 iMock = MockFindOverlapsWithServeralIntervals_case6_7() |
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87 iMock.write(self._inputGff3FileName) |
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88 self._sortAndBuild() |
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89 self._writeExpHFileCase6_7() |
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90 self._writeExpLFileCase6_7() |
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91 self.assertTrue(FileUtils.are2FilesIdentical(self._expHFileName, self._ncList._hFileName)) |
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92 self.assertTrue(FileUtils.are2FilesIdentical(self._expLFileName, self._ncList._lFileName)) |
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93 |
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94 def test_case8(self): |
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95 iMock = MockFindOverlapsWithServeralIntervals_case8() |
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96 iMock.write(self._inputGff3FileName) |
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97 self._sortAndBuild() |
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98 self._writeExpHFileCase8() |
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99 self._writeExpLFileCase8() |
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100 self.assertTrue(FileUtils.are2FilesIdentical(self._expHFileName, self._ncList._hFileName)) |
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101 self.assertTrue(FileUtils.are2FilesIdentical(self._expLFileName, self._ncList._lFileName)) |
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102 |
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103 def test_case9(self): |
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104 iMock = MockFindOverlapsWithServeralIntervals_case9() |
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105 iMock.write(self._inputGff3FileName) |
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106 self._sortAndBuild() |
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107 self._writeExpHFileCase9() |
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108 self._writeExpLFileCase9() |
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109 self.assertTrue(FileUtils.are2FilesIdentical(self._expHFileName, self._ncList._hFileName)) |
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110 self.assertTrue(FileUtils.are2FilesIdentical(self._expLFileName, self._ncList._lFileName)) |
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111 |
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112 def test_case10(self): |
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113 iMock = MockFindOverlapsWithServeralIntervals_case10() |
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114 iMock.write(self._inputGff3FileName) |
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115 self._sortAndBuild() |
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116 self._writeExpHFileCase10() |
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117 self._writeExpLFileCase10() |
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118 self.assertTrue(FileUtils.are2FilesIdentical(self._expHFileName, self._ncList._hFileName)) |
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119 self.assertTrue(FileUtils.are2FilesIdentical(self._expLFileName, self._ncList._lFileName)) |
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120 |
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121 def test_case11(self): |
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122 iMock = MockFindOverlapsWithServeralIntervals_case11() |
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123 iMock.write(self._inputGff3FileName) |
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124 self._sortAndBuild() |
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125 self._writeExpHFileCase11() |
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126 self._writeExpLFileCase11() |
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127 self.assertTrue(FileUtils.are2FilesIdentical(self._expHFileName, self._ncList._hFileName)) |
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128 self.assertTrue(FileUtils.are2FilesIdentical(self._expLFileName, self._ncList._lFileName)) |
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129 |
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130 def test_case12(self): |
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131 iMock = MockFindOverlapsWithServeralIntervals_case12() |
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132 iMock.write(self._inputGff3FileName) |
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133 self._sortAndBuild() |
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134 self._writeExpHFileCase12() |
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135 self._writeExpLFileCase12() |
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136 self.assertTrue(FileUtils.are2FilesIdentical(self._expHFileName, self._ncList._hFileName)) |
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137 self.assertTrue(FileUtils.are2FilesIdentical(self._expLFileName, self._ncList._lFileName)) |
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138 |
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139 def _writeGFF3File(self, fileName): |
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140 f = open(fileName, "w") |
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141 f.write("chr1\ttest\ttest2.1\t9\t1000\t1001\t+\t.\tID=test2.1;Name=test2.1\n") |
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142 f.write("chr1\ttest\ttest2.2\t50\t350\t301\t+\t.\tID=test2.2;Name=test2.2\n") |
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143 f.write("chr1\ttest\ttest2.3\t100\t600\t501\t+\t.\tID=test2.3;Name=test2.3\n") |
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144 f.write("chr1\ttest\ttest2.4\t200\t450\t251\t+\t.\tID=test2.4;Name=test2.4\n") |
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145 f.write("chr1\ttest\ttest2.5\t700\t950\t251\t+\t.\tID=test2.5;Name=test2.5\n") |
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146 f.write("chr1\ttest\ttest2.6\t800\t900\t101\t+\t.\tID=test2.6;Name=test2.6\n") |
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147 f.write("chr1\ttest\ttest2.7\t1200\t1300\t101\t+\t.\tID=test2.7;Name=test2.7\n") |
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148 f.close() |
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149 |
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150 def _writeBinFile(self, fileName, elements): |
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151 handle = open(fileName, "wb") |
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152 for element in elements: |
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153 handle.write(struct.pack('l', element)) |
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154 handle.close() |
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155 |
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156 def _writeExpHFile(self, HFileName): |
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157 list = [0, 2, 48, 3, -1, -1, -1, -1, 120, 1, 144, 1, -1, -1, -1, -1] |
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158 H = open(HFileName, 'wb') |
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159 |
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160 for item in list: |
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161 item = struct.pack('l', item) |
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162 H.write(item) |
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163 H.close() |
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164 |
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165 def _writeExpHFile_with_empty_SubParentDict(self, HFileName): |
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166 list = [0, 1, -1, -1] |
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167 H = open(HFileName, 'wb') |
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168 |
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169 for item in list: |
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170 item = struct.pack('l', item) |
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171 H.write(item) |
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172 H.close() |
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173 |
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174 def _writeExpHFile_one_elementSubList(self): |
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175 elements = [0, 1] |
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176 self._writeBinFile(self._expHFileName, elements) |
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177 |
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178 def _writeExpHFileCase1(self): |
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179 elements = [0, 2, 2, 3, 5, 1, 6, 1] |
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180 self._writeBinFile(self._expHFileName, elements) |
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181 |
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182 def _writeExpHFileCase2(self): |
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183 elements = [0, 2, 2, 1, 3, 1, 4, 1] |
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184 self._writeBinFile(self._expHFileName, elements) |
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185 |
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186 def _writeExpHFileCase3(self): |
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187 elements = [0, 2, 2, 1, 3, 1, 4, 2] |
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188 self._writeBinFile(self._expHFileName, elements) |
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189 |
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190 def _writeExpHFileCase4_5(self): |
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191 elements = [0, 1, 1, 1, 2, 1] |
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192 self._writeBinFile(self._expHFileName, elements) |
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193 |
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194 def _writeExpHFileCase6_7(self): |
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195 elements = [0, 1, 1, 4] |
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196 self._writeBinFile(self._expHFileName, elements) |
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197 |
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198 def _writeExpHFileCase8(self): |
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199 elements = [0, 1, 1, 2] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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200 self._writeBinFile(self._expHFileName, elements) |
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201 |
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202 def _writeExpHFileCase9(self): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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203 elements = [0, 2, 2, 1] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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204 self._writeBinFile(self._expHFileName, elements) |
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205 |
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206 def _writeExpHFileCase10(self): |
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207 elements = [0, 3, 3, 3] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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208 self._writeBinFile(self._expHFileName, elements) |
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209 |
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210 def _writeExpHFileCase11(self): |
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211 elements = [0, 2, 2, 2, 4, 2] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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212 self._writeBinFile(self._expHFileName, elements) |
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213 |
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214 def _writeExpHFileCase12(self): |
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215 elements = [0, 1, 1, 3, 4, 1] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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216 self._writeBinFile(self._expHFileName, elements) |
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217 |
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218 def _writeExpLFile_one_elementSubList(self): |
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219 elements = [0, 1000, 0, -1, -1] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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220 self._writeBinFile(self._expLFileName, elements) |
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221 |
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222 def _writeExpLFileCase1(self): |
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223 elements = [ 0, 1000, 0, 1, -1, \ |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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224 1200, 1300, 2345, -1, -1, \ |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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225 50, 350, 391, -1, 0, \ |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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226 100, 600, 781, 2, 0, \ |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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|
227 700, 950, 1563, 3, 0, \ |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
228 200, 450, 1172, -1, 3, \ |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
229 800, 900, 1954, -1, 4] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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230 self._writeBinFile(self._expLFileName, elements) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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231 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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232 def _writeExpLFileCase2(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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233 elements = [ 0, 500, 0, 1, -1, \ |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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changeset
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234 900, 1200, 1561, -1, -1, \ |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
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235 50, 450, 389, 2, 0, \ |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
236 100, 400, 779, 3, 2, \ |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
237 100, 200, 1170, -1, 3] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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|
238 self._writeBinFile(self._expLFileName, elements) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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239 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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240 def _writeExpLFileCase3(self): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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241 elements = [ 0, 500, 0, 1, -1, \ |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
242 800, 1000, 1952, -1, -1, \ |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
243 50, 450, 389, 2, 0, \ |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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changeset
|
244 100, 400, 779, 3, 2, \ |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
245 100, 200, 1170, -1, 3, \ |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
246 300, 400, 1561, -1, 3] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
247 self._writeBinFile(self._expLFileName, elements) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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248 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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249 def _writeExpLFileCase4_5(self): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
250 elements = [ 0, 1000, 0, 1, -1, \ |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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251 200, 800, 391, 2, 0, \ |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
252 400, 600, 782, -1, 1] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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253 self._writeBinFile(self._expLFileName, elements) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
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254 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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255 def _writeExpLFileCase6_7(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
256 elements = [ 0, 1000, 0, 1, -1, \ |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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changeset
|
257 100, 300, 391, -1, 0, \ |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
258 400, 500, 782, -1, 0, \ |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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changeset
|
259 510, 520, 1173, -1, 0, \ |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
260 850, 950, 1563, -1, 0] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
261 self._writeBinFile(self._expLFileName, elements) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
262 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
263 def _writeExpLFileCase8(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
264 elements = [ 0, 1000, 0, 1, -1, \ |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
265 100, 200, 391, -1, 0, \ |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
266 300, 400, 782, -1, 0] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
267 self._writeBinFile(self._expLFileName, elements) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
268 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
269 def _writeExpLFileCase9(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
270 elements = [ 0, 1000, 0, 1, -1, \ |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
271 800, 1200, 782, -1, -1, \ |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
272 600, 700, 391, -1, 0] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
273 self._writeBinFile(self._expLFileName, elements) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
274 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
275 def _writeExpLFileCase10(self): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
276 elements = [ 0, 1000, 0, 1, -1, \ |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
277 1200, 1300, 1576, -1, -1, \ |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
278 1400, 1500, 1972, -1, -1, \ |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
279 100, 200, 394, -1, 0, \ |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
280 300, 400, 788, -1, 0, \ |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
281 500, 600, 1182, -1, 0] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
282 self._writeBinFile(self._expLFileName, elements) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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changeset
|
283 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
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|
284 def _writeExpLFileCase11(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
285 elements = [ 0, 500, 0, 1, -1, \ |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
286 700, 900, 1180, 2, -1, \ |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
287 100, 200, 392, -1, 0, \ |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
288 300, 400, 786, -1, 0, \ |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
289 710, 720, 1574, -1, 1, \ |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
290 740, 750, 1967, -1, 1] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
291 self._writeBinFile(self._expLFileName, elements) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
292 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
293 def _writeExpLFileCase12(self): |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
294 elements = [ 0, 1400, 0, 1, -1, \ |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
295 300, 500, 368, 2, 0, \ |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
296 800, 1100, 1106, -1, 0, \ |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
297 1200, 1300, 1476, -1, 0, \ |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
298 300, 500, 737, -1, 1] |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
299 self._writeBinFile(self._expLFileName, elements) |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
300 |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
diff
changeset
|
301 if __name__ == "__main__": |
e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
yufei-luo
parents:
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|
302 unittest.main() |