Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/commons/core/parsing/test/Test_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 from commons.core.parsing.CrossSsrAndBesMappedByBlatToGff import CrossSsrAndBesMappedByBlatToGff |
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2 from commons.core.parsing.SsrParser import SsrParser |
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3 |
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4 import unittest |
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5 import os |
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6 |
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7 |
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8 class Test_CrossSsrAndBesMappedByBlatToGff(unittest.TestCase): |
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9 |
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10 |
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11 def test_createDictOfSsrParser(self): |
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12 obsDictSsrParser = {} |
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13 |
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14 ssrFileName = 'input_SSR_Resuts.tab' |
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15 SSRFile = open(ssrFileName, 'w') |
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16 SSRFile.write('BES_name\tBES_redundancy\tSSR_di/tri/tetranucleotide\tSSR_Motif\tSSR_Motif_number\tSSR_start\tSSR_end\tBES_size\n') |
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17 SSRFile.write('MRRE1H001A12RM1\t1\t4\tttta\t6\t272\t295\t724\n') |
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18 SSRFile.write('MRRE1H001B01RM1\t1\t3\taat\t8\t264\t287\t683\n') |
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19 SSRFile.write('MRRE1H001B07RM1\t1\t2\tta\t19\t153\t190\t734\n') |
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20 SSRFile.write('MRRE1H001B07RM1\t2\t2\taata\t25\t83\t90\t734\n') |
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21 SSRFile.close() |
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22 |
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23 iCrossSsrAndBesMappedByBlatToGff = CrossSsrAndBesMappedByBlatToGff() |
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24 iCrossSsrAndBesMappedByBlatToGff._inputFileSSR = ssrFileName |
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25 obsDictSsrParser = iCrossSsrAndBesMappedByBlatToGff.createDictOfSsrParser(obsDictSsrParser) |
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26 |
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27 SsrParser1 = SsrParser('MRRE1H001A12RM1', '1', '4', 'ttta', '6', '272', '295', '724') |
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28 SsrParser2 = SsrParser('MRRE1H001B01RM1', '1', '3', 'aat', '8', '264', '287', '683') |
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29 SsrParser3 = SsrParser('MRRE1H001B07RM1', '1', '2', 'ta', '19', '153', '190', '734') |
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30 SsrParser4 = SsrParser('MRRE1H001B07RM1', '2', '2', 'aata', '25', '83', '90', '734') |
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31 |
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32 expDictSsrParser = { |
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33 'MRRE1H001A12RM1': [SsrParser1], |
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34 'MRRE1H001B01RM1': [SsrParser2], |
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35 'MRRE1H001B07RM1': [SsrParser3, SsrParser4] |
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36 } |
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37 |
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38 self.assertEquals(expDictSsrParser, obsDictSsrParser) |
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39 os.remove(ssrFileName) |
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40 |
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41 def test_convertSSRPositionsToBlatPositions_strand_FW(self): |
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42 ssrPos = 75 |
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43 blatPosStart = 10501475 |
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44 blatPosEnd = 10501985 |
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45 strand = '+' |
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46 iCrossSsrAndBesMappedByBlatToGff = CrossSsrAndBesMappedByBlatToGff() |
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47 obsNewPos = iCrossSsrAndBesMappedByBlatToGff.convertSSRPositionsToChromPositions(ssrPos, blatPosStart, blatPosEnd, strand) |
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48 expNewPos = 10501549 |
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49 self.assertEquals(expNewPos, obsNewPos) |
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50 |
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51 def test_convertSSRPositionsToBlatPositions_strand_RV(self): |
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52 ssrPos = 75 |
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53 blatPosStart = 10501475 |
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54 blatPosEnd = 10501985 |
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55 strand = '-' |
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56 iCrossSsrAndBesMappedByBlatToGff = CrossSsrAndBesMappedByBlatToGff() |
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57 obsNewPos = iCrossSsrAndBesMappedByBlatToGff.convertSSRPositionsToChromPositions(ssrPos, blatPosStart, blatPosEnd, strand) |
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58 expNewPos = 10501911 |
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59 self.assertEquals(expNewPos, obsNewPos) |
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60 |
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61 def test_getSsrMotif(self): |
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62 ssrMotif = 'atg' |
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63 ssrNbMotif = 4 |
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64 iCrossSsrAndBesMappedByBlatToGff = CrossSsrAndBesMappedByBlatToGff() |
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65 obsSsrSeq = iCrossSsrAndBesMappedByBlatToGff.getSsrSeq(ssrMotif, ssrNbMotif) |
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66 expSsrSeq = 'atgatgatgatg' |
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67 self.assertEquals(expSsrSeq, obsSsrSeq) |
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68 |
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69 if __name__ == "__main__": |
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70 unittest.main() |