Mercurial > repos > yufei-luo > s_mart
comparison smart_toolShed/commons/core/writer/MySqlTranscriptWriter.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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-1:000000000000 | 0:e0f8dcca02ed |
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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 os | |
31 import random | |
32 from SMART.Java.Python.mySql.MySqlTable import MySqlTable | |
33 from SMART.Java.Python.mySql.MySqlTranscriptTable import MySqlTranscriptTable | |
34 from SMART.Java.Python.misc.Progress import Progress | |
35 | |
36 class MySqlTranscriptWriter(object): | |
37 """ | |
38 A class that writes a transcript list into a mySQL table | |
39 @ivar name: name of the tables | |
40 @type name: string | |
41 @ivar tables: the tables | |
42 @type tables: dict of L{MySqlTranscriptTable<MySqlTranscriptTable>} | |
43 @ivar mySqlConnection: connection to a MySQL database | |
44 @type mySqlConnection: class L{MySqlConnection<MySqlConnection>} | |
45 @ivar tmpTranscriptFileHandles: files where transcripts are temporary stored, before copy into database | |
46 @type tmpTranscriptFileHandles: dict of file handles | |
47 @ivar nbTranscriptsByChromosome: number of transcripts written | |
48 @type nbTranscriptsByChromosome: dict of int (one for each chromosome) | |
49 @ivar randomNumber: a random number, used for having a unique name for the tables | |
50 @type randomNumber: int | |
51 @ivar toBeWritten: there exists transcripts to be copied into database | |
52 @type toBeWritten: bool | |
53 @ivar verbosity: verbosity | |
54 @type verbosity: int | |
55 """ | |
56 | |
57 | |
58 def __init__(self, connection, name = None, verbosity = 0): | |
59 """ | |
60 Constructor | |
61 @param name: name of the file | |
62 @type name: string | |
63 @param verbosity: verbosity | |
64 @type verbosity: int | |
65 """ | |
66 self.name = name | |
67 self.verbosity = verbosity | |
68 self.tables = {} | |
69 self.indices = {} | |
70 self.tmpTranscriptFileHandles = {} | |
71 self.nbTranscriptsByChromosome = {} | |
72 self.toBeWritten = False | |
73 self.randomNumber = random.randint(0, 100000) | |
74 self.mySqlConnection = connection | |
75 self.nbTmpFiles = 100 | |
76 self.transcriptValues = {} | |
77 self.nbTranscriptValues = 1000 | |
78 if self.name != None: | |
79 pos = self.name.rfind(os.sep) | |
80 if pos != -1: | |
81 self.name = self.name[pos+1:] | |
82 | |
83 | |
84 def __del__(self): | |
85 """ | |
86 Destructor | |
87 Possibly write into into database the last transcripts | |
88 """ | |
89 if self.toBeWritten: | |
90 self.write() | |
91 | |
92 | |
93 def addIndex(self, name, values): | |
94 """ | |
95 Add an index to the tables | |
96 @param name: name of the index | |
97 @type name: string | |
98 @param values: values to index | |
99 @type values: list of strings | |
100 """ | |
101 self.indices[name] = values | |
102 | |
103 | |
104 def createTable(self, chromosome): | |
105 """ | |
106 Create a table for a chromosome | |
107 @param chromosome: a chromosome name | |
108 @type chromosome: string | |
109 """ | |
110 self.tables[chromosome] = MySqlTranscriptTable(self.mySqlConnection, self.name, chromosome, self.verbosity) | |
111 self.tables[chromosome].createTranscriptTable() | |
112 for name, values in self.indices.iteritems(): | |
113 self.tables[chromosome].createIndex("%s_%s_%d" % (name, chromosome, self.randomNumber), values) | |
114 | |
115 | |
116 | |
117 def addTranscript(self, transcript): | |
118 """ | |
119 Add a transcript to the list of transcripts to be written | |
120 @param transcript: transcript to be written | |
121 @type transcript: class L{Transcript<Transcript>} | |
122 """ | |
123 chromosome = transcript.getChromosome() | |
124 if chromosome not in self.tables: | |
125 self.createTable(chromosome) | |
126 self.nbTranscriptsByChromosome[chromosome] = 1 | |
127 if chromosome not in self.transcriptValues: | |
128 self.transcriptValues[chromosome] = [] | |
129 | |
130 self.transcriptValues[chromosome].append(transcript.getSqlValues()) | |
131 | |
132 self.nbTranscriptsByChromosome[chromosome] += 1 | |
133 self.toBeWritten = True | |
134 if sum([len(transcripts) for transcripts in self.transcriptValues.values()]) > self.nbTranscriptValues: | |
135 self.write() | |
136 | |
137 | |
138 def addElement(self, element): | |
139 """ | |
140 Same as "addTranscript" | |
141 @param element: transcript to be written | |
142 @type element: class L{Transcript<Transcript>} | |
143 """ | |
144 self.addTranscript(element) | |
145 | |
146 | |
147 # def addTranscriptList(self, transcriptListParser): | |
148 # """ | |
149 # Add a list of transcripts to the transcripts to be written | |
150 # @param transcriptListParser: transcripts to be written | |
151 # @type transcriptListParser: class L{TranscriptListParser<TranscriptListParser>} | |
152 # """ | |
153 # progress = Progress(transcriptListParser.getNbTranscripts(), "Storing %s into database" % (transcriptListParser.fileName), self.verbosity) | |
154 # for transcript in transcriptListParser.getIterator(): | |
155 # self.addTranscript(transcript) | |
156 # progress.inc() | |
157 # progress.done() | |
158 | |
159 | |
160 def addTranscriptList(self, transcriptListParser): | |
161 """ | |
162 Add a list of transcripts to the transcripts to be written | |
163 @param transcriptListParser: transcripts to be written | |
164 @type transcriptListParser: class L{TranscriptListParser<TranscriptListParser>} | |
165 """ | |
166 self.transcriptListParser = transcriptListParser | |
167 self.mySqlConnection.executeManyQueriesIterator(self) | |
168 | |
169 | |
170 def getIterator(self): | |
171 """ | |
172 Iterator to the SQL commands to insert the list | |
173 """ | |
174 progress = Progress(self.transcriptListParser.getNbTranscripts(), "Storing %s into database" % (self.transcriptListParser.fileName), self.verbosity) | |
175 for transcript in self.transcriptListParser.getIterator(): | |
176 chromosome = transcript.getChromosome() | |
177 if chromosome not in self.tables: | |
178 self.createTable(chromosome) | |
179 self.nbTranscriptsByChromosome[chromosome] = self.nbTranscriptsByChromosome.get(chromosome, 0) + 1 | |
180 values = transcript.getSqlValues() | |
181 yield "INSERT INTO '%s' (%s) VALUES (%s)" % (self.tables[chromosome].name, ", ".join(self.tables[chromosome].variables), ", ".join([MySqlTable.formatSql(values[variable], self.tables[chromosome].types[variable], self.tables[chromosome].sizes[variable]) for variable in self.tables[chromosome].variables])) | |
182 progress.inc() | |
183 progress.done() | |
184 | |
185 | |
186 def write(self): | |
187 """ | |
188 Copy the content of the files into the database | |
189 (May add transcripts to already created databases) | |
190 """ | |
191 for chromosome in self.transcriptValues: | |
192 if chromosome in self.transcriptValues: | |
193 self.tables[chromosome].insertMany(self.transcriptValues[chromosome]) | |
194 self.transcriptValues = {} | |
195 self.toBeWritten = False | |
196 | |
197 | |
198 def getTables(self): | |
199 """ | |
200 Get the tables | |
201 @return: the mySQL tables | |
202 """ | |
203 if self.toBeWritten: | |
204 self.write() | |
205 return self.tables | |
206 | |
207 | |
208 | |
209 def removeTables(self): | |
210 """ | |
211 Drop the tables | |
212 """ | |
213 for chromosome in self.tables: | |
214 self.tables[chromosome].remove() |