Mercurial > repos > yufei-luo > s_mart

comparison 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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-1:000000000000 0:e0f8dcca02ed
1 #
2 # Copyright INRA-URGI 2009-2010
3 #
4 # This software is governed by the CeCILL license under French law and
5 # abiding by the rules of distribution of free software. You can use,
6 # modify and/ or redistribute the software under the terms of the CeCILL
7 # license as circulated by CEA, CNRS and INRIA at the following URL
8 # "http://www.cecill.info".
9 #
10 # As a counterpart to the access to the source code and rights to copy,
11 # modify and redistribute granted by the license, users are provided only
12 # with a limited warranty and the software's author, the holder of the
13 # economic rights, and the successive licensors have only limited
14 # liability.
15 #
16 # In this respect, the user's attention is drawn to the risks associated
17 # with loading, using, modifying and/or developing or reproducing the
18 # software by the user in light of its specific status of free software,
19 # that may mean that it is complicated to manipulate, and that also
20 # therefore means that it is reserved for developers and experienced
21 # professionals having in-depth computer knowledge. Users are therefore
22 # encouraged to load and test the software's suitability as regards their
23 # requirements in conditions enabling the security of their systems and/or
24 # data to be ensured and, more generally, to use and operate it in the
25 # same conditions as regards security.
26 #
27 # The fact that you are presently reading this means that you have had
28 # knowledge of the CeCILL license and that you accept its terms.
29 #
30 import random
31 from SMART.Java.Python.structure.Interval import Interval
32 from SMART.Java.Python.mySql.MySqlTable import MySqlTable
33
34
35 class MySqlExonTable(MySqlTable):
36 """A table of exon in a mySQL database"""
37
38 def __init__(self, connection, name = None, chromosome = None, verbosity = 0):
39 if chromosome == None:
40 chromosome = ""
41 else:
42 chromosome = "_%s" % chromosome
43 if name == None:
44 name = "TmpTable_%d" % (random.randint(0, 100000))
45 name = "%s%s_exons" % (name, chromosome)
46 super(MySqlExonTable, self).__init__(connection, name, verbosity)
47
48
49 def createExonTable(self):
50 variables = Interval.getSqlVariables()
51 variables.append("transcriptId")
52 types = Interval.getSqlTypes()
53 types["transcriptId"] = "int"
54 sizes = Interval.getSqlSizes()
55 sizes["transcriptId"] = 11
56 self.create(variables, types, sizes)
57
58
59 def rename(self, name):
60 super(MySqlExonTable, self).rename("%s_exons" % name)
61
62
63 def addExon(self, exon, transcriptId):
64 values = exon.getSqlValues()
65 values["transcriptId"] = transcriptId
66 id = self.addLine(values)
67 exon.id = id
68
69
70 def retrieveExonsFromTranscriptId(self, transcriptId):
71 if not self.created:
72 return []
73 query = self.mySqlConnection.executeQuery("SELECT * FROM %s WHERE transcriptId = %d" % (self.name, transcriptId))
74 exons = []
75 for exonLine in query.getIterator():
76 exon = Interval()
77 exon.setSqlValues(exonLine)
78 exons.append(exon)
79 return exons
80
81
82 def retrieveExonsFromBulkTranscriptIds(self, transcriptIds):
83 if not transcriptIds:
84 return {}
85 if not self.created:
86 return {}
87 exons = dict([(transcriptId, []) for transcriptId in transcriptIds])
88 query = self.mySqlConnection.executeQuery("SELECT * FROM %s WHERE transcriptId IN (%s)" % (self.name, ", ".join(["%s" % (transcriptId) for transcriptId in transcriptIds])))
89 for exonLine in query.getIterator():
90 exon = Interval()
91 exon.setSqlValues(exonLine)
92 exons[exonLine[-1]].append(exon)
93 return exons
94
95
96 def removeFromTranscriptId(self, transcriptId):
97 self.mySqlConnection.executeQuery("DELETE FROM %s WHERE transcriptId = %d" % (self.name, transcriptId))