Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/commons/core/coord/MergedRange.py @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 # Copyright INRA (Institut National de la Recherche Agronomique)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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2 # http://www.inra.fr
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3 # http://urgi.versailles.inra.fr
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4 #
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5 # This software is governed by the CeCILL license under French law and
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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6 # abiding by the rules of distribution of free software. You can use,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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7 # modify and/ or redistribute the software under the terms of the CeCILL
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8 # license as circulated by CEA, CNRS and INRIA at the following URL
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9 # "http://www.cecill.info".
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10 #
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11 # As a counterpart to the access to the source code and rights to copy,
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12 # modify and redistribute granted by the license, users are provided only
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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13 # with a limited warranty and the software's author, the holder of the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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14 # economic rights, and the successive licensors have only limited
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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15 # liability.
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16 #
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17 # In this respect, the user's attention is drawn to the risks associated
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18 # with loading, using, modifying and/or developing or reproducing the
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19 # software by the user in light of its specific status of free software,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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20 # that may mean that it is complicated to manipulate, and that also
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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21 # therefore means that it is reserved for developers and experienced
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22 # professionals having in-depth computer knowledge. Users are therefore
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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23 # encouraged to load and test the software's suitability as regards their
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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24 # requirements in conditions enabling the security of their systems and/or
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25 # data to be ensured and, more generally, to use and operate it in the
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26 # same conditions as regards security.
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27 #
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28 # The fact that you are presently reading this means that you have had
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29 # knowledge of the CeCILL license and that you accept its terms.
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30
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31 ## Record a region on multiple sequence using Path ID information
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32 #
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33 class MergedRange(object):
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34
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35 ## Constructor
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36 #
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37 # @param lId list of Path ID
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38 # @param start the start coordinate
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39 # @param end the end coordinate
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40 #
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41 def __init__(self, lId = None, start = -1, end = -1):
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42 self._lId = lId or []
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43 self._start = start
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44 self._end = end
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45
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46 ## Equal operator
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47 #
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48 # @param o a MergedRange instance
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49 #
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50 def __eq__(self, o):
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51 return o._lId == self._lId and o._start == self._start and o._end == self._end
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52
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53
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54 ## Return True if the MergedRange instance overlaps with another MergedRange instance, False otherwise
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55 #
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56 # @param o a MergedRange instance
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57 # @return boolean False or True
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58 #
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59 def isOverlapping(self, o):
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60 if o._start <= self._start and o._end >= self._end:
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61 return True
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62 if o._start >= self._start and o._start <= self._end or o._end >= self._start and o._end <= self._end:
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63 return True
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64 return False
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65
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66 ## Merge coordinates and ID of two Merged Range
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67 #
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68 # @param o a MergedRange instance
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69 #
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70 def merge(self, o):
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71 self._start = min(self._start, o._start)
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72 self._end = max(self._end, o._end)
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73 self._lId.extend(o._lId)
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74 self._lId.sort()
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75
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76 ## Set a Merged Range instance using a Match instance
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77 #
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78 # @param iMatch instance Match instance
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79 #
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80 def setFromMatch(self, iMatch):
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81 self._lId= [iMatch.id]
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82 self._start = iMatch.range_query.start
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83 self._end = iMatch.range_query.end
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84
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85 ## Get a Merged Range instance list using a Match instance list
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86 #
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87 # @param lIMatch list Match instance list
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88 # @return lMergedRange list MergedRange instance list
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89 #
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90 def getMergedRangeListFromMatchList(lIMatch):
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91 lMergedRange = []
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92 for iMatch in lIMatch:
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93 mr = MergedRange()
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94 mr.setFromMatch(iMatch)
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95 lMergedRange.append(mr)
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96 return lMergedRange
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97
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98 getMergedRangeListFromMatchList = staticmethod(getMergedRangeListFromMatchList)