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comparison commons/tools/TEclassifierPE.py @ 18:94ab73e8a190

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author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
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17:b0e8584489e6 18:94ab73e8a190
1 #!/usr/bin/env python
2
3 # Copyright INRA (Institut National de la Recherche Agronomique)
4 # http://www.inra.fr
5 # http://urgi.versailles.inra.fr
6 #
7 # This software is governed by the CeCILL license under French law and
8 # abiding by the rules of distribution of free software. You can use,
9 # modify and/ or redistribute the software under the terms of the CeCILL
10 # license as circulated by CEA, CNRS and INRIA at the following URL
11 # "http://www.cecill.info".
12 #
13 # As a counterpart to the access to the source code and rights to copy,
14 # modify and redistribute granted by the license, users are provided only
15 # with a limited warranty and the software's author, the holder of the
16 # economic rights, and the successive licensors have only limited
17 # liability.
18 #
19 # In this respect, the user's attention is drawn to the risks associated
20 # with loading, using, modifying and/or developing or reproducing the
21 # software by the user in light of its specific status of free software,
22 # that may mean that it is complicated to manipulate, and that also
23 # therefore means that it is reserved for developers and experienced
24 # professionals having in-depth computer knowledge. Users are therefore
25 # encouraged to load and test the software's suitability as regards their
26 # requirements in conditions enabling the security of their systems and/or
27 # data to be ensured and, more generally, to use and operate it in the
28 # same conditions as regards security.
29 #
30 # The fact that you are presently reading this means that you have had
31 # knowledge of the CeCILL license and that you accept its terms.
32
33 import os
34 import sys
35
36 if not "REPET_PATH" in os.environ.keys():
37 print "ERROR: no environment variable REPET_PATH"
38 sys.exit(1)
39 sys.path.append(os.environ["REPET_PATH"])
40 if not "PYTHONPATH" in os.environ.keys():
41 os.environ["PYTHONPATH"] = os.environ["REPET_PATH"]
42 else:
43 os.environ["PYTHONPATH"] = "%s:%s" % (os.environ["REPET_PATH"], os.environ["PYTHONPATH"])
44
45 from commons.core.LoggerFactory import LoggerFactory
46 from commons.core.utils.RepetOptionParser import RepetOptionParser
47 from commons.core.checker.ConfigChecker import ConfigRules
48 from commons.core.checker.ConfigChecker import ConfigChecker
49 from commons.core.seq.FastaUtils import FastaUtils
50 from denovo_pipe.ReverseComplementAccordingToClassif import ReverseComplementAccordingToClassif
51 from denovo_pipe.RenameHeaderClassif import RenameHeaderClassif
52 from denovo_pipe.DetectTEFeatures import DetectTEFeatures
53 from denovo_pipe.LaunchPASTEC import LaunchPASTEC
54 from PASTEC.StatPastec import StatPastec
55
56 LOG_DEPTH = "repet.tools"
57 #LOG_FORMAT = "%(message)s"
58
59 ####TEclassifier PASTEC Edition
60 #
61 class TEclassifierPE(object):
62
63 def __init__(self, fastaFileName = "", configFileName = "", addWickerCode = False, reverseComp = False, doClean = False, verbosity = 0):
64 self._fastaFileName = fastaFileName
65 self._addWickerCode = addWickerCode
66 self._reverseComp = reverseComp
67 self._configFileName = configFileName
68 self._doClean = doClean
69 self._verbosity = verbosity
70 self._projectName = ""
71 self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
72
73 def setAttributesFromCmdLine(self):
74 description = "TE classifier PASTEC Edition.\n"
75 description += "Detect TE features on consensus and classify them. Give some classification statistics.\n"
76 description += "Can rename headers with classification info and Wicker's code at the beginning.\n"
77 description += "Can reverse-complement consensus if they are detected in reverse strand.\n"
78 description += "Warning : it's highly advised to use sequences in upper case.\n"
79 epilog = "\n"
80 epilog += "Example 1: launch and clean temporary files\n"
81 epilog += "\t$ python TEclassifierPE.py -i consensus.fa -C TEclassifier.cfg -c\n"
82 epilog += "\n"
83 epilog += "Example 2: launch with 'rename headers' and 'reverse-complement' options\n"
84 epilog += "\t$ python TEclassifierPE.py -i consensus.fa -C TEclassifier.cfg -c -w -r\n"
85 parser = RepetOptionParser(description = description, epilog = epilog)
86 parser.add_option("-i", "--fasta", dest = "fastaFileName", action = "store", type = "string", help = "input fasta file name [compulsory] [format: fasta]", default = "")
87 parser.add_option("-C", "--config", dest = "configFileName",action = "store", type = "string", help = "configuration file name (e.g. TEclassifier.cfg) [compulsory]", default = "")
88 parser.add_option("-w", "--wicker", dest = "addWickerCode", action = "store_true", help = "add classification info and Wicker's code at the beginning of the headers [optional] [default: False]", default = False)
89 parser.add_option("-r", "--reverse", dest = "reverseComp", action = "store_true", help = "reverse-complement consensus if they are detected in reverse strand [optional] [default: False]", default = False)
90 parser.add_option("-c", "--clean", dest = "doClean", action = "store_true", help = "clean temporary files [optional] [default: False]", default = False)
91 parser.add_option("-v", "--verbosity", dest = "verbosity", action = "store", type = "int", help = "verbosity [optional] [default: 3, from 1 to 4]", default = 3)
92 options = parser.parse_args()[0]
93 self._setAttributesFromOptions(options)
94
95 def _setAttributesFromOptions(self, options):
96 self.setFastaFileName(options.fastaFileName)
97 self.setAddWickerCode(options.addWickerCode)
98 self.setReverseComp(options.reverseComp)
99 self.setConfigFileName(options.configFileName)
100 self.setDoClean(options.doClean)
101 self.setVerbosity(options.verbosity)
102
103 def _checkConfig(self):
104 iConfigRules = ConfigRules()
105 iConfigRules.addRuleOption(section="project", option ="project_name", mandatory=True, type="string")
106 sectionName = "classif_consensus"
107 iConfigRules.addRuleOption(section=sectionName, option ="clean", mandatory=True, type="bool")
108 iConfigChecker = ConfigChecker(self._configFileName, iConfigRules)
109 iConfig = iConfigChecker.getConfig()
110 self._setAttributesFromConfig(iConfig)
111
112 def _setAttributesFromConfig(self, iConfig):
113 self.setProjectName(iConfig.get("project", "project_name"))
114 sectionName = "classif_consensus"
115 self.setDoClean(iConfig.get(sectionName, "clean"))
116
117 def setFastaFileName(self, fastaFileName):
118 self._fastaFileName = fastaFileName
119
120 def setConfigFileName(self, configFileName):
121 self._configFileName = configFileName
122
123 def setAddWickerCode(self, addWickerCode):
124 self._addWickerCode = addWickerCode
125
126 def setReverseComp(self, reverseComp):
127 self._reverseComp = reverseComp
128
129 def setDoClean(self, doClean):
130 self._doClean = doClean
131
132 def setVerbosity(self, verbosity):
133 self._verbosity = verbosity
134
135 def setProjectName(self, projectName):
136 self._projectName = projectName
137
138 def _checkOptions(self):
139 if self._fastaFileName == "":
140 self._logAndRaise("ERROR: Missing input fasta file name")
141
142 def _logAndRaise(self, errorMsg):
143 self._log.error(errorMsg)
144 raise Exception(errorMsg)
145
146 def run(self):
147 LoggerFactory.setLevel(self._log, self._verbosity)
148 if self._configFileName:
149 self._checkConfig()
150 self._checkOptions()
151 self._log.info("START TEclassifier PASTEC Edition")
152 self._log.debug("Fasta file name: %s" % self._fastaFileName)
153 nbSeq = FastaUtils.dbSize(self._fastaFileName)
154 self._log.debug("Total number of sequences: %i)" % nbSeq)
155
156 #TODO: add step => avoid to re-launch DetectTEFeatures, if error with PASTEC (e.g. wrong bank format)
157 #step 1
158 iDF = DetectTEFeatures(self._fastaFileName, self._projectName, self._configFileName, self._doClean, self._verbosity)
159 iDF.run()
160
161 #step 2
162 iLP = LaunchPASTEC(configFileName = self._configFileName, inputFileName = self._fastaFileName, projectName = self._projectName, verbose = self._verbosity)
163 iLP.run()
164
165 classifFileName = "%s.classif" % self._projectName
166
167 iSP = StatPastec(classifFileName)
168 iSP.run()
169
170 if self._reverseComp:
171 self._log.info("Reverse complement...")
172 iRevComplAccording2Classif = ReverseComplementAccordingToClassif()
173 iRevComplAccording2Classif.setFastaFile(self._fastaFileName)
174 iRevComplAccording2Classif.setClassifFile(classifFileName)
175 iRevComplAccording2Classif.run()
176 tmpFastaFileName = "%s_negStrandReversed.fa" % os.path.splitext(self._fastaFileName)[0]
177 else:
178 tmpFastaFileName = self._fastaFileName
179
180 if self._addWickerCode:
181 self._log.info("Rename headers according to Wicker's code...")
182 iRHC = RenameHeaderClassif(classifFileName, tmpFastaFileName, self._projectName)
183 iRHC.setOutputFileName("")
184 iRHC.run()
185 if self._doClean:
186 os.remove(tmpFastaFileName)
187
188 self._log.info("END TEclassifier PASTEC Edition")
189
190 if __name__ == "__main__":
191 iLaunch = TEclassifierPE()
192 iLaunch.setAttributesFromCmdLine()
193 iLaunch.run()