18
+ − 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 MATCHER
+ − 40 #
+ − 41 class LaunchMatcher(object):
+ − 42
+ − 43 def __init__(self, align="", queryFileName="", subjectFileName="", evalue="1e-10", doJoin=False, keepConflict=False, prefix="", doClean = False, verbosity = 0):
+ − 44 self._alignFileName = align
+ − 45 self._queryFileName = queryFileName
+ − 46 self.setSubjectFileName(subjectFileName)
+ − 47 self.setOutPrefix(prefix)
+ − 48 self._doJoin = doJoin
+ − 49 self._eValue = evalue
+ − 50 self._keepConflict = keepConflict
+ − 51
+ − 52 self._doClean = doClean
+ − 53 self._verbosity = verbosity
+ − 54 self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
+ − 55
+ − 56 def setAttributesFromCmdLine(self):
+ − 57 description = "Launch Matcher."
+ − 58 epilog = "\nExample 1: launch without verbosity and keep temporary files.\n"
+ − 59 epilog += "\t$ python LaunchMatcher.py -a in.align -v 0"
+ − 60 epilog += "\n\t"
+ − 61 epilog += "\nExample 2: launch with verbosity to have errors (level 1) and basic information (level 2), and delete temporary files.\n"
+ − 62 epilog += "\t$ python LaunchMatcher.py -a in.align -q query.fa -s nr.fa -c -v 2"
+ − 63 parser = RepetOptionParser(description = description, epilog = epilog)
+ − 64 parser.add_option("-a", "--align", dest = "align", action = "store", type = "string", help = "input align file name [compulsory] [format: align]", default = "")
+ − 65 parser.add_option("-q", "--query", dest = "query", action = "store", type = "string", help = "query fasta file name [optional] [format: fasta]", default = "")
+ − 66 parser.add_option("-s", "--subject", dest = "subject", action = "store", type = "string", help = "subject fasta file name [optional] [format: fasta]", default = "")
+ − 67 parser.add_option("-e", "--evalue", dest = "evalue", action = "store", type = "string", help = "E-value filter [default: 1e-10]", default = "1e-10")
+ − 68 parser.add_option("-j", "--join", dest = "doJoin", action = "store_true", help = "join matches [default: False]", default = False)
+ − 69 parser.add_option("-k", "--keepConflict",dest = "keepConflict", action = "store_true", help = "keep conflicting subjects [default: False]", default = False)
+ − 70 parser.add_option("-o", "--outPrefix", dest = "outPrefix", action = "store", type = "string", help = "output file prefix [default: align file name]", default = "")
+ − 71 parser.add_option("-c", "--clean", dest = "doClean", action = "store_true", help = "clean temporary files [default: False]", default = False)
+ − 72 parser.add_option("-v", "--verbosity", dest = "verbosity", action = "store", type = "int", help = "verbosity [default: 1]", default = 1)
+ − 73 options = parser.parse_args()[0]
+ − 74 self._setAttributesFromOptions(options)
+ − 75
+ − 76 def _setAttributesFromOptions(self, options):
+ − 77 self.setAlignFileName(options.align)
+ − 78 self.setQueryFileName(options.query)
+ − 79 self.setSubjectFileName(options.subject)
+ − 80 self.setEvalue(options.evalue)
+ − 81 self.setDoJoin(options.doJoin)
+ − 82 self.setKeepConflicts(options.keepConflict)
+ − 83 self.setOutPrefix(options.outPrefix)
+ − 84 self.setDoClean(options.doClean)
+ − 85 self.setVerbosity(options.verbosity)
+ − 86
+ − 87 def setAlignFileName(self, alignFileName):
+ − 88 self._alignFileName = alignFileName
+ − 89
+ − 90 def setQueryFileName(self, queryFileName):
+ − 91 self._queryFileName = queryFileName
+ − 92
+ − 93 def setSubjectFileName(self, subjectFileName):
+ − 94 self._subjectFileName = subjectFileName
+ − 95
+ − 96 def setEvalue(self, evalue):
+ − 97 self._eValue = evalue
+ − 98
+ − 99 def setDoJoin(self, doJoin):
+ − 100 self._doJoin = doJoin
+ − 101
+ − 102 def setKeepConflicts(self, keepConflict):
+ − 103 self._keepConflict = keepConflict
+ − 104
+ − 105 def setOutPrefix(self, outPrefix):
+ − 106 if outPrefix == "":
+ − 107 self._outPrefix = self._alignFileName
+ − 108 else:
+ − 109 self._outPrefix = outPrefix
+ − 110
+ − 111 def setDoClean(self, doClean):
+ − 112 self._doClean = doClean
+ − 113
+ − 114 def setVerbosity(self, verbosity):
+ − 115 self._verbosity = verbosity
+ − 116
+ − 117 def _checkOptions(self):
+ − 118 if self._alignFileName == "":
+ − 119 self._logAndRaise("ERROR: Missing input align file name")
+ − 120
+ − 121 def _logAndRaise(self, errorMsg):
+ − 122 self._log.error(errorMsg)
+ − 123 raise Exception(errorMsg)
+ − 124
+ − 125 def _getMatcherCmd(self):
+ − 126 lArgs = []
+ − 127 lArgs.append("-m %s" % self._alignFileName)
+ − 128 if self._queryFileName:
+ − 129 lArgs.append("-q %s" % self._queryFileName)
+ − 130 if self._subjectFileName:
+ − 131 lArgs.append("-s %s" % self._subjectFileName)
+ − 132 if self._doJoin:
+ − 133 lArgs.append("-j")
+ − 134 lArgs.append("-E %s" % self._eValue)
+ − 135 lArgs.append("-B %s" % self._outPrefix)
+ − 136 if self._keepConflict:
+ − 137 lArgs.append("-a")
+ − 138 lArgs.append("-v %i" % (self._verbosity - 1))
+ − 139 return self._getSystemCommand("matcher", lArgs)
+ − 140
+ − 141 def _getSystemCommand(self, prg, lArgs):
+ − 142 systemCmd = prg
+ − 143 for arg in lArgs:
+ − 144 systemCmd += " " + arg
+ − 145 return systemCmd
+ − 146
+ − 147 def run(self):
+ − 148 LoggerFactory.setLevel(self._log, self._verbosity)
+ − 149 self._checkOptions()
+ − 150 self._log.info("START LaunchMatcher")
+ − 151 self._log.debug("Align file name: %s" % self._alignFileName)
+ − 152 self._log.debug("Query file name: %s" % self._queryFileName)
+ − 153 self._log.debug("Subject file name: %s" % self._subjectFileName)
+ − 154 #TODO: clean files
+ − 155 # if self._doClean:
+ − 156 # self._log.warning("Files will be cleaned")
+ − 157 cmd = self._getMatcherCmd()
+ − 158 process = subprocess.Popen(cmd, shell = True)
+ − 159 self._log.debug("Running : %s" % cmd)
+ − 160 process.communicate()
+ − 161 if process.returncode != 0:
+ − 162 self._logAndRaise("ERROR when launching '%s'" % cmd)
+ − 163 self._log.info("END LaunchMatcher")
+ − 164
+ − 165 if __name__ == "__main__":
+ − 166 iLaunch = LaunchMatcher()
+ − 167 iLaunch.setAttributesFromCmdLine()
+ − 168 iLaunch.run()
