Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/parsing/test/Test_F_CrossSsrAndBesMappedByBlatToGff.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 unittest |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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2 import os |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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3 from commons.core.utils.FileUtils import FileUtils |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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4 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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5 class Test_F_CrossSsrAndBesMappedByBlatToGff(unittest.TestCase): |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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6 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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7 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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8 def test_run(self): |
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9 ssrInputFileName = '%s/commons/core/parsing/test/ssrInputFile.tab' % os.environ['REPET_PATH'] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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10 self._writeSsrInputFile(ssrInputFileName) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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11 blatInputFileName = '%s/commons/core/parsing/test/blatInputFile.tab' % os.environ['REPET_PATH'] |
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12 self._writeBlatInputFile(blatInputFileName) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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13 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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14 obsOutputFileName = '%s/commons/core/parsing/test/obsOutputFile.tab' % os.environ['REPET_PATH'] |
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15 cmd = 'python %s/commons/core/parsing/CrossSsrAndBesMappedByBlatToGff.py -s %s -b %s -o %s' % (os.environ['REPET_PATH'], ssrInputFileName, blatInputFileName, obsOutputFileName) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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16 os.system(cmd) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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17 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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18 expOutputFileName = '%s/commons/core/parsing/test/expOutputFile.tab' % os.environ['REPET_PATH'] |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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19 self._writeExpOutputFile(expOutputFileName) |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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20 |
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21 self.assertTrue(FileUtils.are2FilesIdentical(expOutputFileName, obsOutputFileName)) |
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22 os.remove(ssrInputFileName) |
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23 os.remove(blatInputFileName) |
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24 os.remove(obsOutputFileName) |
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25 os.remove(expOutputFileName) |
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26 |
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27 def _writeBlatInputFile(self, blatInputFileName): |
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28 file = open(blatInputFileName, 'w') |
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29 file.write('psLayout version 3\n') |
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30 file.write('\n') |
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31 file.write('match mis- rep. N\'s Q gap Q gap T gap T gap strand Q Q Q Q T T T T block blockSizes qStarts tStarts\n') |
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32 file.write(' match match count bases count bases name size start end name size start end count\n') |
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33 file.write('---------------------------------------------------------------------------------------------------------------------------------------------------------------\n') |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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34 file.write('315\t20\t0\t0\t3\t10\t2\t9\t+\tMRRE1H001H13FM1\t378\t0\t345\tchr16\t22053297\t21686950\t21687294\t4\t76,185,7,67,\t0,77,263,278,\t21686950,21687026,21687213,21687227,\n') |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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35 file.write('690\t11\t0\t0\t1\t3\t2\t4\t-\tmachin1\t704\t0\t704\tchr16\t22053297\t21736364\t21737069\t3\t40,647,14,\t0,43,690,\t21736364,21736406,21737055,\n') |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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36 file.write('554\t26\t0\t0\t1\t16\t1\t17\t-\tMRRE1H032F08FM1\t606\t10\t606\tchr11\t19818926\t3725876\t3726473\t2\t553,27,\t10,579,\t3725876,3726446,\n') |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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37 file.write('620\t23\t0\t0\t0\t0\t0\t0\t-\tmachin2\t643\t0\t643\tchr11\t19818926\t3794984\t3795627\t1\t643,\t0,\t3794984,\n') |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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38 file.write('347\t25\t0\t0\t0\t0\t0\t0\t-\tmachin3\t393\t21\t393\tchr18\t29360087\t12067347\t12067719\t1\t372,\t0,\t12067347,\n') |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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39 file.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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40 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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41 def _writeSsrInputFile(self, ssrInputFileName): |
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42 file = open(ssrInputFileName, 'w') |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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43 file.write('BES_name BES_redundancy SSR_di/tri/tetranucleotide SSR_Motif SSR_Motif_number SSR_start SSR_end BES_size\n') |
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44 file.write('truc1\t1\t4\tttta\t6\t272\t295\t724\n') |
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45 file.write('truc2\t1\t3\taat\t8\t264\t287\t683\n') |
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46 file.write('MRRE1H001H13FM1\t1\t2\tta\t19\t153\t190\t378\n') |
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47 file.write('truc3\t2\t4\taaag\t8\t518\t549\t734\n') |
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48 file.write('MRRE1H032F08FM1\t1\t4\taaat\t7\t544\t571\t606\n') |
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49 file.write('MRRE1H032F08FM1\t2\t2\tag\t10\t587\t606\t606\n') |
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50 file.write('truc4\t1\t2\tat\t16\t519\t550\t672\n') |
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51 file.write('truc5\t1\t3\ttct\t8\t205\t228\t752\n') |
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52 file.write('truc6\t1\t2\tat\t33\t287\t352\t569\n') |
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53 file.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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54 |
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55 def _writeExpOutputFile(self, expOutputFileName): |
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56 file = open(expOutputFileName, 'w') |
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57 file.write('##gff-version 3\n') |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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58 file.write('chr16\tCrossSsrAndBesAlignedByBlat\tSSR\t21687102\t21687139\t.\t+\t.\tID=SSR_MRRE1H001H13FM1_1;Name=SSR_MRRE1H001H13FM1_1;bes_name=MRRE1H001H13FM1;bes_size=378;bes_matchstart=0;bes_matchend=345;bes_redundancy=1;ssr_type=2;ssr_motif=ta;ssr_motif_number=19;ssr_start=153;ssr_end=190;muscadine_seq=tatatatatatatatatatatatatatatatatatata\n') |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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59 file.write('chr11\tCrossSsrAndBesAlignedByBlat\tSSR\t3725930\t3725903\t.\t-\t.\tID=SSR_MRRE1H032F08FM1_1;Name=SSR_MRRE1H032F08FM1_1;bes_name=MRRE1H032F08FM1;bes_size=606;bes_matchstart=10;bes_matchend=606;bes_redundancy=1;ssr_type=4;ssr_motif=aaat;ssr_motif_number=7;ssr_start=544;ssr_end=571;muscadine_seq=aaataaataaataaataaataaataaat\n') |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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60 file.write('chr11\tCrossSsrAndBesAlignedByBlat\tSSR\t3725887\t3725868\t.\t-\t.\tID=SSR_MRRE1H032F08FM1_2;Name=SSR_MRRE1H032F08FM1_2;bes_name=MRRE1H032F08FM1;bes_size=606;bes_matchstart=10;bes_matchend=606;bes_redundancy=2;ssr_type=2;ssr_motif=ag;ssr_motif_number=10;ssr_start=587;ssr_end=606;muscadine_seq=agagagagagagagagagag\n') |
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61 file.close() |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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62 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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63 if __name__ == "__main__": |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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64 unittest.main() |
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65 |
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66 |