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comparison commons/tools/LaunchBlaster.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 from commons.core.LoggerFactory import LoggerFactory
34 from commons.core.utils.RepetOptionParser import RepetOptionParser
35 import subprocess
36
37 LOG_DEPTH = "repet.tools"
38
39 ##Launch BLASTER
40 #
41 class LaunchBlaster(object):
42
43 def __init__(self, queryFileName = "", subjectFileName = "", evalue = 1e-300, identity = 90, length = 100, doAllByall = False, type = "ncbi", nbCPU = 1, program="blastn",extraParams="", doClean = False, verbosity = 0):
44 self._queryFileName = queryFileName
45 self.setSubjectFileName(subjectFileName)
46 self._eValue = evalue
47 self._identity = identity
48 self._length = length
49 self._doAllByall = doAllByall
50 self._blastType = type
51 self._program = program
52 self._extraParams = extraParams
53 self._nbCPU = nbCPU
54 self._doClean = doClean
55 self._verbosity = verbosity
56 self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
57
58 def setAttributesFromCmdLine(self):
59 description = "Launch Blaster."
60 epilog = "\nExample 1: launch without verbosity and keep temporary files.\n"
61 epilog += "\t$ python LaunchBlaster.py -q query.fa -v 0"
62 epilog += "\n\t"
63 epilog += "\nExample 2: launch with verbosity to have errors (level 1) and basic information (level 2), and delete temporary files.\n"
64 epilog += "\t$ python LaunchBlaster.py -q query.fa -s nr.fa -c -v 2"
65 parser = RepetOptionParser(description = description, epilog = epilog)
66 parser.add_option("-q", "--query", dest = "query", action = "store", type = "string", help = "query fasta file name [compulsory] [format: fasta]", default = "")
67 parser.add_option("-s", "--subject", dest = "subject", action = "store", type = "string", help = "subject fasta file name [default: query] [format: fasta]", default = "")
68 parser.add_option("-e", "--evalue", dest = "evalue", action = "store", type = "string", help = "Blast e-value [default: 1e-300]", default = "1e-300")
69 parser.add_option("-d", "--id", dest = "identity", action = "store", type = "int", help = "Blast identity [default: 90]", default = 90)
70 parser.add_option("-l", "--length", dest = "length", action = "store", type = "int", help = "Minimal hit length [default: 100]", default = 100)
71 parser.add_option("-a", "--aba", dest = "doAllByall", action = "store_true", help = "all-by-all Blast [default: False]", default = False)
72 parser.add_option("-t", "--type", dest = "type", action = "store", type = "string", help = "Blast type [ncbi, wu, blastplus] [default: ncbi]", default = "ncbi")
73 parser.add_option("-u", "--program", dest = "program", action = "store", type = "string", help = "Blast program type [blastn, blastx, blastx] [default: blastn]", default = "blastn")
74 parser.add_option("-x", "--extraParams",dest = "extraParams", action = "store", type = "string", help = "Additional blast program parameters[default: '']", default = "")
75 parser.add_option("-n", "--ncpu", dest = "cpu", action = "store", type = "int", help = "Number of CPUs to use [default: 1]", default = 1)
76 parser.add_option("-c", "--clean", dest = "doClean", action = "store_true", help = "clean temporary files [default: False]", default = False)
77 parser.add_option("-v", "--verbosity", dest = "verbosity", action = "store", type = "int", help = "verbosity [default: 1]", default = 1)
78 options = parser.parse_args()[0]
79 self._setAttributesFromOptions(options)
80
81 def _setAttributesFromOptions(self, options):
82 self.setQueryFileName(options.query)
83 self.setSubjectFileName(options.subject)
84 self.setEvalue(options.evalue)
85 self.setIdentity(options.identity)
86 self.setLength(options.length)
87 self.setDoAllByall(options.doAllByall)
88 self.setType(options.type)
89 self.setProgram(options.program)
90 self.setExtraParams(options.extraParams)
91 self.setCPU(options.cpu)
92 self.setDoClean(options.doClean)
93 self.setVerbosity(options.verbosity)
94
95
96 def setQueryFileName(self, queryFileName):
97 self._queryFileName = queryFileName
98
99 def setSubjectFileName(self, subjectFileName):
100 if subjectFileName == "":
101 self._subjectFileName = self._queryFileName
102 else:
103 self._subjectFileName = subjectFileName
104
105 def setEvalue(self, evalue):
106 self._eValue = evalue
107
108 def setIdentity(self, identity):
109 self._identity = identity
110
111 def setLength(self, length):
112 self._length = length
113
114 def setDoAllByall(self, doAllByall):
115 self._doAllByall = doAllByall
116
117 def setType(self, blastType):
118 self._blastType = blastType
119
120 def setProgram(self, program):
121 self._program = program
122
123 def setExtraParams(self, extraParams):
124 self._extraParams = extraParams
125
126 def setCPU(self, cpu):
127 self._nbCPU = cpu
128
129 def setDoClean(self, doClean):
130 self._doClean = doClean
131
132 def setVerbosity(self, verbosity):
133 self._verbosity = verbosity
134
135 def _checkOptions(self):
136 if self._queryFileName == "":
137 self._logAndRaise("ERROR: Missing input fasta file name")
138
139 lBlastType = ["ncbi", "wu", "blastplus"]
140 if self._blastType.lower() not in lBlastType:
141 self._logAndRaise("ERROR: unknown Blast type '%s' - correct values are %s" % (self._blastType, lBlastType))
142
143 def _logAndRaise(self, errorMsg):
144 self._log.error(errorMsg)
145 raise Exception(errorMsg)
146
147 def _getBlasterCmd(self):
148 lArgs = []
149 lArgs.append("-n %s" % self._program)
150 lArgs.append("-q %s" % self._queryFileName)
151 lArgs.append("-s %s" % self._subjectFileName)
152 lArgs.append("-B %s" % self._queryFileName)
153 if self._doAllByall:
154 lArgs.append("-a")
155 lArgs.append("-E %s" % self._eValue)
156 lArgs.append("-L %s" % self._length)
157 lArgs.append("-I %s" % self._identity)
158 if self._blastType == "ncbi":
159 lArgs.append("-N")
160 lArgs.append("-p '-a %s %s'" % (self._nbCPU, self._extraParams))
161 elif self._blastType == "wu":
162 lArgs.append("-W")
163 lArgs.append("-p '-cpus=%s %s'" % (self._nbCPU, self._extraParams))
164 elif self._blastType == "blastplus":
165 lArgs.append("-X")
166 lArgs.append("-p '-num_threads %s %s'" % (self._nbCPU, self._extraParams))
167 # TODO: check the check option at the beginning of step 2 to allow to launch megablast for blast and blast+
168 # elif config.get(sectionName, "blast") == "mega":
169 # lArgs.append("-N")
170 # lArgs.append("-n megablast")
171 # elif config.get(sectionName, "blast") == "megablastplus":
172 # lArgs.append("-X")
173 # lArgs.append("-n megablast")
174 if self._doClean:
175 lArgs.append("-c")
176 lArgs.append("-v %i" % (self._verbosity - 1))
177 return self._getSystemCommand("blaster", lArgs)
178
179 def _getSystemCommand(self, prg, lArgs):
180 systemCmd = prg
181 for arg in lArgs:
182 systemCmd += " " + arg
183 return systemCmd
184
185 def run(self):
186 LoggerFactory.setLevel(self._log, self._verbosity)
187 self._checkOptions()
188 self._log.info("START LaunchBlaster")
189 self._log.debug("Query file name: %s" % self._queryFileName)
190 self._log.debug("Subject file name: %s" % self._subjectFileName)
191 if self._doClean:
192 self._log.warning("Files will be cleaned")
193 cmd = self._getBlasterCmd()
194 process = subprocess.Popen(cmd, shell = True)
195 self._log.debug("Running : %s" % cmd)
196 process.communicate()
197 if process.returncode != 0:
198 self._logAndRaise("ERROR when launching '%s'" % cmd)
199 self._log.info("END LaunchBlaster")
200
201 if __name__ == "__main__":
202 iLaunch = LaunchBlaster()
203 iLaunch.setAttributesFromCmdLine()
204 iLaunch.run()