Mercurial > repos > yufei-luo > s_mart
comparison SMART/Java/Python/ClusterizeByTags.py @ 6:769e306b7933
Change the repository level.
author | yufei-luo |
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date | Fri, 18 Jan 2013 04:54:14 -0500 |
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5:ea3082881bf8 | 6:769e306b7933 |
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1 #! /usr/bin/env python | |
2 # | |
3 # Copyright INRA-URGI 2009-2011 | |
4 # | |
5 # This software is governed by the CeCILL license under French law and | |
6 # abiding by the rules of distribution of free software. You can use, | |
7 # modify and/ or redistribute the software under the terms of the CeCILL | |
8 # license as circulated by CEA, CNRS and INRIA at the following URL | |
9 # "http://www.cecill.info". | |
10 # | |
11 # As a counterpart to the access to the source code and rights to copy, | |
12 # modify and redistribute granted by the license, users are provided only | |
13 # with a limited warranty and the software's author, the holder of the | |
14 # economic rights, and the successive licensors have only limited | |
15 # liability. | |
16 # | |
17 # In this respect, the user's attention is drawn to the risks associated | |
18 # with loading, using, modifying and/or developing or reproducing the | |
19 # software by the user in light of its specific status of free software, | |
20 # that may mean that it is complicated to manipulate, and that also | |
21 # therefore means that it is reserved for developers and experienced | |
22 # professionals having in-depth computer knowledge. Users are therefore | |
23 # encouraged to load and test the software's suitability as regards their | |
24 # requirements in conditions enabling the security of their systems and/or | |
25 # data to be ensured and, more generally, to use and operate it in the | |
26 # same conditions as regards security. | |
27 # | |
28 # The fact that you are presently reading this means that you have had | |
29 # knowledge of the CeCILL license and that you accept its terms. | |
30 # | |
31 import random | |
32 from optparse import OptionParser | |
33 from commons.core.parsing.ParserChooser import ParserChooser | |
34 from commons.core.writer.TranscriptWriter import TranscriptWriter | |
35 from SMART.Java.Python.structure.Transcript import Transcript | |
36 from SMART.Java.Python.structure.Interval import Interval | |
37 from SMART.Java.Python.misc.Progress import Progress | |
38 from SMART.Java.Python.mySql.MySqlConnection import MySqlConnection | |
39 from commons.core.writer.MySqlTranscriptWriter import MySqlTranscriptWriter | |
40 | |
41 | |
42 OPERATIONS = ("diff", "div") | |
43 BOOLTOSTRANDS = {True: [0], False: [-1, 1]} | |
44 | |
45 class ClusterizeByTags(object): | |
46 | |
47 def __init__(self, verbosity): | |
48 self.verbosity = verbosity | |
49 self.connection = MySqlConnection(self.verbosity-1) | |
50 self.defautValue = None | |
51 self.maxDistance = None | |
52 self.oneStrand = False | |
53 | |
54 def setInputFile(self, fileName, format): | |
55 chooser = ParserChooser(self.verbosity) | |
56 chooser.findFormat(format) | |
57 parser = chooser.getParser(fileName) | |
58 writer = MySqlTranscriptWriter(self.connection, None, self.verbosity) | |
59 writer.addTranscriptList(parser) | |
60 writer.write() | |
61 self.transcriptTables = writer.getTables() | |
62 | |
63 def setOutputFile(self, fileName): | |
64 self.writer = TranscriptWriter(fileName, "gff3", self.verbosity) | |
65 | |
66 def setTag(self, tagName, defaultValue): | |
67 self.tagName = tagName | |
68 self.defaultValue = defaultValue | |
69 | |
70 def setThreshold(self, threshold): | |
71 self.threshold = threshold | |
72 | |
73 def setOperation(self, operation): | |
74 self.operation = operation | |
75 if self.operation not in OPERATIONS: | |
76 raise Exception("Operation '%s' unsupported: choose among %s" % (self.operation, ", ".join(OPERATIONS))) | |
77 | |
78 def setMaxDistance(self, distance): | |
79 self.maxDistance = distance | |
80 | |
81 def setOneStrand(self, oneStrand): | |
82 self.oneStrand = oneStrand | |
83 | |
84 def run(self): | |
85 for chromosome in sorted(self.transcriptTables.keys()): | |
86 progress = Progress(self.transcriptTables[chromosome].getNbElements(), "Analyzing %s" % (chromosome), self.verbosity) | |
87 for strand in BOOLTOSTRANDS[self.oneStrand]: | |
88 previousValue = None | |
89 previousTrend = None | |
90 previousTranscript = None | |
91 sumValue = 0 | |
92 command = "SELECT * FROM %s" % (self.transcriptTables[chromosome].getName()) | |
93 if not self.oneStrand: | |
94 command += " WHERE direction = %d" % (strand) | |
95 command += " ORDER BY start, end" | |
96 for index, transcript in self.transcriptTables[chromosome].selectTranscripts(command): | |
97 if self.tagName in transcript.getTagNames(): | |
98 value = transcript.getTagValue(self.tagName) | |
99 else: | |
100 value = self.defaultValue | |
101 if previousValue == None: | |
102 trend = None | |
103 else: | |
104 if self.operation == "diff": | |
105 trend = value - previousValue | |
106 else: | |
107 trend = value / previousValue | |
108 if previousTranscript == None: | |
109 sumValue = value | |
110 elif (previousTrend == None or abs(trend - previousTrend) <= self.threshold) and (self.maxDistance == None or previousTranscript.getDistance(transcript) <= self.maxDistance) and (previousTranscript.getDirection() == transcript.getDirection() or not self.oneStrand): | |
111 if previousTranscript.getDirection() != transcript.getDirection(): | |
112 transcript.reverse() | |
113 previousTranscript.merge(transcript) | |
114 transcript = previousTranscript | |
115 sumValue += value | |
116 previousTrend = trend | |
117 else: | |
118 previousTranscript.setTagValue(self.tagName, sumValue) | |
119 self.writer.addTranscript(previousTranscript) | |
120 sumValue = value | |
121 previousTrend = None | |
122 previousValue = value | |
123 previousTranscript = transcript | |
124 progress.inc() | |
125 if previousTranscript != None: | |
126 previousTranscript.setTagValue(self.tagName, sumValue) | |
127 self.writer.addTranscript(previousTranscript) | |
128 progress.done() | |
129 self.writer.close() | |
130 | |
131 | |
132 if __name__ == "__main__": | |
133 | |
134 description = "Clusterize By Tags v1.0.1: Clusterize a set of element using their tag values. [Category: Merge]" | |
135 | |
136 parser = OptionParser(description = description) | |
137 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="query input file [compulsory] [format: file in transcript format given by -f]") | |
138 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of previous file [compulsory] [format: transcript file format]") | |
139 parser.add_option("-t", "--tag", dest="tagName", action="store", type="string", help="name of the tag [format: string] [compulsory]") | |
140 parser.add_option("-e", "--default", dest="defaultValue", action="store", default=None, type="int", help="default value for the tag [format: string]") | |
141 parser.add_option("-r", "--threshold", dest="threshold", action="store", type="int", help="threshold between two consecutive tags [format: int] [compulsory]") | |
142 parser.add_option("-p", "--operation", dest="operation", action="store", type="string", help="operation to apply between 2 different clusters to compare them [format: choice (diff, div)] [compulsory]") | |
143 parser.add_option("-d", "--distance", dest="maxDistance", action="store", default=None, type="int", help="maximum distance for 2 clusters to be merged [format: int] [default: None]") | |
144 parser.add_option("-1", "--oneStrand", dest="oneStrand", action="store_true", default=False, help="also cluster the elements which are on different strands [format: bool] [default: False]") | |
145 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [format: output file in GFF3 format]") | |
146 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]") | |
147 (options, args) = parser.parse_args() | |
148 | |
149 cbt = ClusterizeByTags(options.verbosity) | |
150 cbt.setInputFile(options.inputFileName, options.format) | |
151 cbt.setOutputFile(options.outputFileName) | |
152 cbt.setTag(option.tagName, option.defaultValue) | |
153 cbt.setThreshold(option.threshold) | |
154 cbt.setOperation(option.operation) | |
155 cbt.setMaxDistance(operation.maxDistance) | |
156 cbt.setOneStrand(operation.oneStrand) | |
157 cbt.run() |