|
6
|
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 import sys
|
|
|
32 from SMART.Java.Python.structure.TranscriptList import TranscriptList
|
|
|
33 from SMART.Java.Python.mySql.MySqlExonTable import MySqlExonTable
|
|
|
34 from SMART.Java.Python.mySql.MySqlTable import MySqlTable
|
|
|
35 from SMART.Java.Python.structure.Transcript import Transcript
|
|
|
36 from SMART.Java.Python.misc.Progress import Progress
|
|
|
37
|
|
|
38 class MySqlTranscriptTable(MySqlTable):
|
|
|
39 """A table of transcripts in a mySQL database"""
|
|
|
40
|
|
|
41 def __init__(self, connection, name = None, chromosome = None, verbosity = 0):
|
|
|
42 if chromosome == None:
|
|
|
43 chromosome = ""
|
|
|
44 else:
|
|
|
45 chromosome = "_%s" % chromosome
|
|
|
46 if name == None:
|
|
|
47 name = "TmpTable_%d" % (random.randint(0, 100000))
|
|
|
48 name = "%s%s" % (name, chromosome)
|
|
|
49 super(MySqlTranscriptTable, self).__init__(connection, "%s_transcripts" % name, verbosity)
|
|
|
50
|
|
|
51
|
|
|
52 def createTranscriptTable(self):
|
|
|
53 self.create(Transcript.getSqlVariables(), Transcript.getSqlTypes(), Transcript.getSqlSizes())
|
|
|
54
|
|
|
55
|
|
|
56 def rename(self, name):
|
|
|
57 super(MySqlTranscriptTable, self).rename("%s_transcripts" % name)
|
|
|
58
|
|
|
59
|
|
|
60 def remove(self):
|
|
|
61 super(MySqlTranscriptTable, self).remove()
|
|
|
62
|
|
|
63
|
|
|
64 def clear(self):
|
|
|
65 super(MySqlTranscriptTable, self).clear()
|
|
|
66
|
|
|
67
|
|
|
68 def copy(self, transcriptTable):
|
|
|
69 self.remove()
|
|
|
70 super(MySqlTranscriptTable, self).copy(transcriptTable)
|
|
|
71
|
|
|
72
|
|
|
73 def add(self, transcriptTable):
|
|
|
74 super(MySqlTranscriptTable, self).add(transcriptTable)
|
|
|
75
|
|
|
76
|
|
|
77 def addTranscript(self, transcript):
|
|
|
78 id = self.addLine(transcript.getSqlValues())
|
|
|
79 transcript.id = id
|
|
|
80
|
|
|
81
|
|
|
82 def addTranscriptList(self, transcriptList):
|
|
|
83 progress = Progress(transcriptList.getNbTranscript(), "Storing list to %s" % (self.name), self.verbosity)
|
|
|
84 for transcript in transcriptList.getIterator():
|
|
|
85 self.addTranscript(transcript)
|
|
|
86 progress.inc()
|
|
|
87 progress.done()
|
|
|
88
|
|
|
89
|
|
|
90 def removeTranscript(self, transcript):
|
|
|
91 self.removeFromId(transcript.id)
|
|
|
92
|
|
|
93
|
|
|
94 def retrieveTranscriptFromId(self, id):
|
|
|
95 transcript = Transcript()
|
|
|
96 transcript.setSqlValues(self.retrieveFromId(id))
|
|
|
97 return transcript
|
|
|
98
|
|
|
99
|
|
|
100 def retrieveBulkTranscriptFromId(self, ids):
|
|
|
101 if not ids:
|
|
|
102 return []
|
|
|
103 transcripts = self.retrieveBulkFromId(ids)
|
|
|
104 idsToTranscripts = {}
|
|
|
105 for values in transcripts:
|
|
|
106 transcript = Transcript()
|
|
|
107 transcript.setSqlValues(values)
|
|
|
108 idsToTranscripts[values[0]] = transcript
|
|
|
109 return idsToTranscripts.values()
|
|
|
110
|
|
|
111
|
|
|
112 def selectTranscripts(self, command, simple = False):
|
|
|
113 MAXSIZE = 100000
|
|
|
114 found = True
|
|
|
115 cpt = 0
|
|
|
116 while found:
|
|
|
117 found = False
|
|
|
118 if simple:
|
|
|
119 thisCommand = command
|
|
|
120 else:
|
|
|
121 thisCommand = "%s LIMIT %d OFFSET %d" % (command, MAXSIZE, MAXSIZE * cpt)
|
|
|
122 query = self.mySqlConnection.executeQuery(thisCommand)
|
|
|
123 for line in query.getIterator():
|
|
|
124 found = True
|
|
|
125 id = int(line[0])
|
|
|
126 transcript = Transcript()
|
|
|
127 transcript.setSqlValues(line)
|
|
|
128 yield (id, transcript)
|
|
|
129 cpt += 1
|
|
|
130 if simple:
|
|
|
131 return
|
|
|
132
|
|
|
133
|
|
|
134 def getIterator(self):
|
|
|
135 for id, transcript in self.selectTranscripts("SELECT * FROM '%s'" % (self.name)):
|
|
|
136 yield transcript
|
|
|
137
|
|
|
138
|
|
|
139 def retrieveTranscriptList(self):
|
|
|
140 transcriptList = TranscriptList()
|
|
|
141 for transcriptLine in self.getLines():
|
|
|
142 transcript = Transcript()
|
|
|
143 transcript.setSqlValues(transcriptLine)
|
|
|
144 transcriptList.addTranscript(transcript)
|
|
|
145 return transcriptList
|
|
|
146
|
|
|
147
|
|
|
148 def setDefaultTagValue(self, name, value):
|
|
18
|
149 super(MySqlTranscriptTable, self).setDefaultTagValue(Transcript.getSqlVariables().index("tags")+1, name, value) |
