Mercurial > repos > yufei-luo > s_mart
annotate smart_toolShed/SMART/Java/Python/structure/SequenceList.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 # |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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2 # Copyright INRA-URGI 2009-2010 |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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3 # |
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4 # This software is governed by the CeCILL license under French law and |
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5 # abiding by the rules of distribution of free software. You can use, |
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6 # modify and/ or redistribute the software under the terms of the CeCILL |
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7 # license as circulated by CEA, CNRS and INRIA at the following URL |
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8 # "http://www.cecill.info". |
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9 # |
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10 # As a counterpart to the access to the source code and rights to copy, |
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11 # modify and redistribute granted by the license, users are provided only |
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12 # with a limited warranty and the software's author, the holder of the |
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13 # economic rights, and the successive licensors have only limited |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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14 # liability. |
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15 # |
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16 # In this respect, the user's attention is drawn to the risks associated |
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17 # with loading, using, modifying and/or developing or reproducing the |
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18 # software by the user in light of its specific status of free software, |
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19 # that may mean that it is complicated to manipulate, and that also |
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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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20 # therefore means that it is reserved for developers and experienced |
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21 # professionals having in-depth computer knowledge. Users are therefore |
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22 # encouraged to load and test the software's suitability as regards their |
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23 # requirements in conditions enabling the security of their systems and/or |
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24 # data to be ensured and, more generally, to use and operate it in the |
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25 # same conditions as regards security. |
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26 # |
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27 # The fact that you are presently reading this means that you have had |
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28 # knowledge of the CeCILL license and that you accept its terms. |
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29 # |
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30 import math |
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31 |
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32 class SequenceList(object): |
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33 """A class that codes for a list of sequences""" |
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34 |
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35 def __init__(self, verbosity = 0): |
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36 self.sequences = [] |
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37 self.verbosity = verbosity |
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38 |
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39 |
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40 def nbSequences(self): |
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41 return len(self.sequences) |
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42 |
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43 |
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44 def getSequence(self, index): |
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45 return self.sequences[index] |
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46 |
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47 |
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48 def addSequence(self, sequence): |
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49 self.sequences.append(sequence) |
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50 |
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51 |
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52 def split(self, number): |
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53 sequenceLists = [] |
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54 size = math.ceil(self.nbSequences() / number) |
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55 |
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56 sequenceList = SequenceList() |
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57 for i in range(0, self.nbSequences()): |
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58 sequenceList.addSequence(self.getSequence(i)) |
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59 if (sequenceList.nbSequences() == size): |
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60 sequenceLists.append(sequenceList) |
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61 sequenceList = SequenceList() |
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62 if (sequenceList.nbSequences() != 0): |
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63 sequenceLists.append(sequenceList) |
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64 return sequenceLists |
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65 |
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66 |
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67 def printFasta(self): |
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68 string = "" |
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69 for sequence in self.sequences: |
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70 string += sequence.printFasta() |
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71 return string |
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72 |