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1 import os
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2 import unittest
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3 from commons.core.utils.FileUtils import FileUtils
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4 from commons.core.sql.DbMySql import DbMySql
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5 from commons.tools.GetSpecificTELibAccordingToAnnotation import GetSpecificTELibAccordingToAnnotation
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6
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7 class Test_GetSpecificTELibAccordingToAnnotation(unittest.TestCase):
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8
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9 def test_writeFastaFileFromGiveInfoTEAnnot(self):
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10 self._iDb = DbMySql()
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11 fileName = "GiveInfoTEannot.txt"
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12 self._writeGiveInfoTEannotOutput(fileName)
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13 tableName = "projectName_refTEs_chr_seq"
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14 self._createConsensusTable(tableName)
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15 expFileName = "consensusExp.fa"
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16 self._writeExpConsensusFile(expFileName)
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17 obsFileName = "%s.fa" % os.path.splitext(fileName)[0]
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18 iGetTElib = GetSpecificTELibAccordingToAnnotation()
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19 iGetTElib.setTableName(tableName)
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20 iGetTElib.writeFastaFileFromGiveInfoTEAnnot(fileName)
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21 self._iDb.dropTable(tableName)
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22 self._iDb.close()
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23 self.assertTrue(FileUtils.are2FilesIdentical(expFileName, obsFileName))
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24 os.remove(fileName)
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25 os.remove(expFileName)
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26 os.remove(obsFileName)
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27
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28 def _writeGiveInfoTEannotOutput(self, fileName):
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29 f = open(fileName, "w")
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30 f.write("TE\tmaxLength\tmeanLength\tcovg\tfrags\tfullLgthFrags\tcopies\tfullLgthCopies\tmeanId\tsdId\tminId\tq25Id\tmedId\tq75Id\tmaxId\tmeanLgth\tsdLgth\tminLgth\tq25Lgth\tmedLgth\tq75Lgth\tmaxLgth\tmeanLgthPerc\tsdLgthPerc\tminLgthPerc\tq25LgthPerc\tmedLgthPerc\tq75LgthPerc\tmaxLgthPerc\n")
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31 f.write("Atha_benchs-B-P66.38-Map20_classII-Helitron-incomp\t2150\t2150\t195657\t158\t49\t152\t52\t84.88\t8.75\t74.29\t77.16\t80.08\t96.40\t97.83\t1287.32\t776.47\t21\t570.00\t1320.50\t2077.00\t2272\t59.88\t36.11\t0.98\t26.51\t61.42\t96.60\t105.67\n")
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32 f.write("Atha_benchs-B-R1047-Map6_classI-LINE-comp\t1653\t1653\t25423\t57\t4\t56\t4\t79.09\t8.21\t64.32\t73.63\t79.21\t83.65\t96.65\t453.98\t488.66\t29\t98.00\t244.00\t634.00\t1650\t27.46\t29.56\t1.75\t5.93\t14.76\t38.35\t99.82\n")
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33 f.write("Atha_benchs-B-R1276-Map4_classII-Helitron-incomp\t1293\t1293\t24416\t48\t4\t47\t4\t80.31\t5.74\t75.14\t77.00\t78.25\t80.89\t99.46\t519.60\t419.01\t37\t171.00\t334.00\t838.00\t1296\t40.19\t32.41\t2.86\t13.23\t25.83\t64.81\t100.23\n")
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34 f.close()
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35
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36 def _createConsensusTable(self, tableName):
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37 fileName = "consensus.fa"
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38 f = open(fileName, "w")
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39 f.write(">Atha_benchs-B-P66.38-Map20_classII-Helitron-incomp\n")
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40 f.write("ATGCTAGCTAGCT\n")
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41 f.write(">Atha_benchs-B-R12-Map5_classII-Helitron-comp\n")
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42 f.write("ATGCTAGCTAGCTATGCTAGCTAGCATGCTAGCTAGCTT\n")
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43 f.write(">Atha_benchs-B-R1047-Map6_classI-LINE-comp\n")
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44 f.write("ATGCTAGCTAGCT\n")
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45 f.write(">Atha_benchs-B-G56-Map5_classII-Helitron-comp\n")
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46 f.write("ATGCTAGCTAGCTATGCTAGCTAGCT\n")
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47 f.write(">Atha_benchs-B-R1276-Map4_classII-Helitron-incomp\n")
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48 f.write("ATGCTAGCTAGCATGCTAGCTAGCTATGCTAGCTAGCTATGCTAGCTAGCTT\n")
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49 f.close()
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50 self._iDb.createTable(tableName, "seq", fileName, True)
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51 os.remove(fileName)
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52
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53 def _writeExpConsensusFile(self, fileName):
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54 f = open(fileName, "w")
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55 f.write(">Atha_benchs-B-P66.38-Map20_classII-Helitron-incomp\n")
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56 f.write("ATGCTAGCTAGCT\n")
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57 f.write(">Atha_benchs-B-R1047-Map6_classI-LINE-comp\n")
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58 f.write("ATGCTAGCTAGCT\n")
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59 f.write(">Atha_benchs-B-R1276-Map4_classII-Helitron-incomp\n")
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60 f.write("ATGCTAGCTAGCATGCTAGCTAGCTATGCTAGCTAGCTATGCTAGCTAGCTT\n")
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61 f.close()
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62
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63 if __name__ == "__main__":
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64 unittest.main() |
