Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/SMART/Java/Python/mySql/MySqlExonTable.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 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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2 # Copyright INRA-URGI 2009-2010
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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3 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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4 # 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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5 # 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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6 # modify and/ or redistribute the software under the terms of the CeCILL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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7 # license as circulated by CEA, CNRS and INRIA at the following URL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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8 # "http://www.cecill.info".
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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9 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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10 # As a counterpart to the access to the source code and rights to copy,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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11 # 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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12 # 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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13 # 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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14 # liability.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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15 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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16 # In this respect, the user's attention is drawn to the risks associated
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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17 # with loading, using, modifying and/or developing or reproducing the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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18 # 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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19 # 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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20 # therefore means that it is reserved for developers and experienced
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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21 # 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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22 # 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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23 # requirements in conditions enabling the security of their systems and/or
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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24 # data to be ensured and, more generally, to use and operate it in the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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25 # same conditions as regards security.
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26 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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27 # The fact that you are presently reading this means that you have had
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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28 # knowledge of the CeCILL license and that you accept its terms.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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29 #
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30 import random
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31 from SMART.Java.Python.structure.Interval import Interval
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32 from SMART.Java.Python.mySql.MySqlTable import MySqlTable
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33
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34
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35 class MySqlExonTable(MySqlTable):
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36 """A table of exon in a mySQL database"""
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37
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38 def __init__(self, connection, name = None, chromosome = None, verbosity = 0):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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39 if chromosome == None:
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40 chromosome = ""
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41 else:
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42 chromosome = "_%s" % chromosome
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43 if name == None:
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44 name = "TmpTable_%d" % (random.randint(0, 100000))
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45 name = "%s%s_exons" % (name, chromosome)
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46 super(MySqlExonTable, self).__init__(connection, name, verbosity)
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47
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48
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49 def createExonTable(self):
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50 variables = Interval.getSqlVariables()
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51 variables.append("transcriptId")
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52 types = Interval.getSqlTypes()
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53 types["transcriptId"] = "int"
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54 sizes = Interval.getSqlSizes()
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55 sizes["transcriptId"] = 11
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56 self.create(variables, types, sizes)
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57
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58
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59 def rename(self, name):
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60 super(MySqlExonTable, self).rename("%s_exons" % name)
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61
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62
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63 def addExon(self, exon, transcriptId):
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64 values = exon.getSqlValues()
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65 values["transcriptId"] = transcriptId
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66 id = self.addLine(values)
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67 exon.id = id
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68
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69
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70 def retrieveExonsFromTranscriptId(self, transcriptId):
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71 if not self.created:
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72 return []
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73 query = self.mySqlConnection.executeQuery("SELECT * FROM %s WHERE transcriptId = %d" % (self.name, transcriptId))
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74 exons = []
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75 for exonLine in query.getIterator():
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76 exon = Interval()
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77 exon.setSqlValues(exonLine)
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78 exons.append(exon)
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79 return exons
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80
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81
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82 def retrieveExonsFromBulkTranscriptIds(self, transcriptIds):
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83 if not transcriptIds:
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84 return {}
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85 if not self.created:
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86 return {}
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87 exons = dict([(transcriptId, []) for transcriptId in transcriptIds])
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88 query = self.mySqlConnection.executeQuery("SELECT * FROM %s WHERE transcriptId IN (%s)" % (self.name, ", ".join(["%s" % (transcriptId) for transcriptId in transcriptIds])))
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89 for exonLine in query.getIterator():
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90 exon = Interval()
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91 exon.setSqlValues(exonLine)
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92 exons[exonLine[-1]].append(exon)
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93 return exons
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94
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95
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96 def removeFromTranscriptId(self, transcriptId):
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97 self.mySqlConnection.executeQuery("DELETE FROM %s WHERE transcriptId = %d" % (self.name, transcriptId))