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1 #! /usr/bin/env python
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2
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3 # Copyright INRA (Institut National de la Recherche Agronomique)
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4 # http://www.inra.fr
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5 # http://urgi.versailles.inra.fr
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6 #
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7 # This software is governed by the CeCILL license under French law and
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8 # abiding by the rules of distribution of free software. You can use,
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9 # modify and/ or redistribute the software under the terms of the CeCILL
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10 # license as circulated by CEA, CNRS and INRIA at the following URL
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11 # "http://www.cecill.info".
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12 #
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13 # As a counterpart to the access to the source code and rights to copy,
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14 # modify and redistribute granted by the license, users are provided only
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15 # with a limited warranty and the software's author, the holder of the
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16 # economic rights, and the successive licensors have only limited
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17 # liability.
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18 #
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19 # In this respect, the user's attention is drawn to the risks associated
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20 # with loading, using, modifying and/or developing or reproducing the
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21 # software by the user in light of its specific status of free software,
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22 # that may mean that it is complicated to manipulate, and that also
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23 # therefore means that it is reserved for developers and experienced
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24 # professionals having in-depth computer knowledge. Users are therefore
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25 # encouraged to load and test the software's suitability as regards their
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26 # requirements in conditions enabling the security of their systems and/or
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27 # data to be ensured and, more generally, to use and operate it in the
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28 # same conditions as regards security.
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29 #
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30 # The fact that you are presently reading this means that you have had
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31 # knowledge of the CeCILL license and that you accept its terms.
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32
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33 from commons.core.checker.CheckerUtils import CheckerUtils
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34 from commons.core.utils.FileUtils import FileUtils
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35 from commons.core.utils.RepetOptionParser import RepetOptionParser
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36 import subprocess
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37 from commons.core.LoggerFactory import LoggerFactory
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38 import os
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39 import shutil
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40
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41 LOG_DEPTH = "repet.tools"
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42
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43 class LaunchMummerPlot(object):
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44
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45 def __init__(self, inputFileName="", queryFileName="", refFileName ="", prefix = None, fat=False, filter=False,clean=False, verbosity=0):
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46 self._inputFileName = inputFileName
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47 self._queryFileName = queryFileName
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48 self._refFileName = refFileName
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49 self._prefix = prefix
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50 self._fat = fat
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51 self._filter = filter
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52 self.doClean = clean
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53 self.verbosity = verbosity
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54 self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self.verbosity)
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55
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56 def setAttributesFromCmdLine(self):
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57 description = "LaunchMummerPlot runs the MummerPlot program (part of the mummer package) ."
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58 parser = RepetOptionParser(description = description)
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59 parser.add_option("-i", "--input", dest="inputFileName", default = None, action="store", type="string", help="input file[mandatory] [format: delta]")
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60 parser.add_option("-q", "--Qfile", dest="queryFileName", default = None, action="store", type="string", help="Plot an ordered set of reference sequences from Qfile [optional] [format: fasta]")
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61 parser.add_option("-r", "--Rfile", dest="refFileName", default = None, action="store", type="string", help="Plot an ordered set of reference sequences from Rfile [optional] [format: fasta]")
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62 parser.add_option("-p", "--prefix", dest="prefix", default = None, action="store", type="string", help="prefix name [mandatory]")
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63 parser.add_option("-o","--fat", dest="fat",action="store_true", help="Layout sequences using fattest alignment only[optional] ")
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64 parser.add_option("-s","--filter", dest="filter",action="store_true", help="Only display .delta alignments which represent the 'best' hit [optional] ")
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65 parser.add_option("-c", "--clean", dest = "clean", help = "clean temporary files", default = False, action="store_true")
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66 parser.add_option("-v", "--verbosity", dest="verbosity", default = 0, action="store", type="int", help="verbosity [optional] ")
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67
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68 (self._options, args) = parser.parse_args()
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69 self._setAttributesFromOptions(self._options)
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70
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71 def _setAttributesFromOptions(self, options):
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72 self._inputFileName = options.inputFileName
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73 self._queryFileName = options.queryFileName
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74 self._refFileName = options.refFileName
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75 self._prefix = options.prefix
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76 self._fat = options.fat
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77 self._filter = options.filter
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78 self.verbosity = options.verbosity
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79
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80 def _logAndRaise(self, errorMsg):
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81 self._log.error(errorMsg)
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82 raise Exception(errorMsg)
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83
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84 def checkOptions(self):
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85 if self._inputFileName != "":
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86 if not FileUtils.isRessourceExists(self._inputFileName):
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87 self._logAndRaise("ERROR: Query file: %s does not exist!" % self._inputFileName)
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88 else:
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89 self._logAndRaise("ERROR: No specified --query option!")
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90
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91 if self._queryFileName != "":
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92 if not FileUtils.isRessourceExists(self._queryFileName):
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93 self._logAndRaise("ERROR: Query file: %s does not exist!" % self._queryFileName)
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94
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95 if self._refFileName != "":
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96 if not FileUtils.isRessourceExists(self._refFileName):
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97 self._logAndRaise("ERROR: Ref file does not exist!"% self._refFileName)
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98
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99 def clean(self):
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100 try:
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101 os.remove("%s.filter" % self._prefix)
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102 except Exception as inst:
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103 self._log.error(inst)
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104 try:
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105 os.remove("%s.fplot" % self._prefix)
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106 except Exception as inst:
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107 self._log.error(inst)
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108 try:
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109 os.remove("%s.rplot" % self._prefix)
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110 except Exception as inst:
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111 self._log.error(inst)
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112
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113 def run(self):
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114 if not CheckerUtils.isExecutableInUserPath("mummerplot") :
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115 self._logAndRaise("ERROR: mummerplot must be in your path")
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116 self.checkOptions()
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117
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118 ref=""
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119 if self._refFileName != "":
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120 ref = "-R %s" % self._refFileName
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121
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122 query=""
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123 if self._queryFileName != "":
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124 query = "-Q %s" % self._queryFileName
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125
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126 fat = ""
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127 if self._fat:
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128 fat = "--fat"
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129
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130 filter = ""
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131 if self._filter:
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132 filter = "-f"
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133
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134 prefix = ""
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135 if self._prefix is not None:
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136 prefix = "--prefix=%s" %(self._prefix)
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137
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138 cmd = "mummerplot %s %s %s %s %s %s --png" % (self._inputFileName, prefix, ref, query, fat, filter)
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139 self._log.debug("Running mummerplot with following commands : %s" %cmd)
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140 cmd = cmd.split()
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141 process = subprocess.Popen(cmd)
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142 process.wait()
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143
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144 self.clean()
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145 return process.returncode
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146
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147 if __name__ == "__main__":
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148 iLaunchNucmer = LaunchMummerPlot()
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149 iLaunchNucmer.setAttributesFromCmdLine()
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150 iLaunchNucmer.run() |
