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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 import sys
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34 import os
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35 import optparse
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36 from commons.core.checker.CheckerUtils import CheckerUtils
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37 from commons.core.utils.FileUtils import FileUtils
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38 from subprocess import Popen
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39 from commons.core.utils.RepetOptionParser import RepetOptionParser
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40 import subprocess
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41 import tempfile
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42
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43 class LaunchLastZ(object):
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44
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45 def __init__(self,queryFileName="", refFileName ="", outputFileName=None,outputFileFormat="axt",noTransition=True, ambiguous=None, step=1,gfextend=False, chain=False, verbosity=1 ):
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46 self.queryFileName = queryFileName
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47 self.refFileName = refFileName
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48 self.outputFileName = outputFileName
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49 self.outputFileFormat = outputFileFormat
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50 self.noTransition = noTransition
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51 self.step = step
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52 self.ambiguous = ambiguous
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53 self.gfextend = gfextend
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54 self.chain = chain
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55 self.verbosity = verbosity
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56
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57 def setAttributesFromCmdLine(self):
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58 description = "LaunchLastZ runs the LastZ program ."
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59 parser = RepetOptionParser(description = description)
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60 parser.add_option("-q", "--query", dest="queryFileName", default = None, action="store", type="string", help="input query file [compulsory] [format: fasta]")
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61 parser.add_option("-r", "--ref", dest="refFileName", default = None, action="store", type="string", help="input ref file [compulsory] [format: fasta]")
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62 parser.add_option("-o", "--output", dest="outputFileName", default = None, action="store", type="string", help="output file [compulsory] ")
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63 parser.add_option("-f", "--format", dest="outputFileFormat", default = "axt", action="store", type="string", help="output file format[optional] ")
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64 parser.add_option("-n", "--notransition", dest="noTransition", action="store_false", default=True, help="noTransition (default True) [optional] ")
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65 parser.add_option("-a", "--ambiguous", dest="ambiguous", action="store", type="string", help="ambiguous [optional] ")
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66 parser.add_option("-s", "--step", dest="step", default = 1, action="store", type="int", help="stepsize (default 1) [optional] ")
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67 parser.add_option("-g", "--gfextend", dest="gfextend", action="store_true", help="extend gf (default false)[optional] ")
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68 parser.add_option("-c", "--chain", dest="chain", action="store_true", help="chain (default false)[optional] ")
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69 parser.add_option("-v", "--verbosity", dest="verbosity", default = 1, action="store", type="int", help="verbosity [optional] ")
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70 (self._options, args) = parser.parse_args()
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71 self._setAttributesFromOptions(self._options)
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72
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73 def _setAttributesFromOptions(self, options):
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74 self.queryFileName = options.queryFileName
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75 self.refFileName = options.refFileName
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76 self.outputFileName = options.outputFileName
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77 self.outputFileFormat = options.outputFileFormat
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78 self.ambiguous = options.ambiguous
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79 self.noTransition = options.noTransition
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80 self.step = options.step
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81 self.gfextend = options.gfextend
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82 self.chain = options.chain
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83 self.verbosity = options.verbosity
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84
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85 def checkOptions(self):
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86 if self.queryFileName != "":
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87 if not FileUtils.isRessourceExists(self.queryFileName):
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88 raise Exception("ERROR: Query file does not exist!")
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89 else:
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90 raise Exception("ERROR: No specified --query option!")
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91 if self.refFileName != "":
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92 if not FileUtils.isRessourceExists(self.refFileName):
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93 raise Exception("ERROR: Ref file does not exist!")
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94 else:
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95 raise Exception("ERROR: No specified --ref option!")
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96 if self.outputFileName == None:
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97 self.outputFileName = "%s_%s.axt" % (os.path.basename(self.queryFileName), os.path.basename(self.refFileName))
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98
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99 def run(self):
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100 if not CheckerUtils.isExecutableInUserPath("lastz") :
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101 print ("ERROR: LastZ must be in your path")
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102 else:
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103 self.checkOptions()
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104
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105 transition = ""
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106 if self.noTransition:
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107 transition = "--notransition"
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108 ambiguous = ""
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109 if self.ambiguous is not None:
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110 ambiguous = "--ambiguous=%s" % self.ambiguous
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111
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112 gfextend = ""
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113 if self.gfextend:
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114 gfextend = "--gfextend"
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115
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116 chain = ""
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117 if self.chain:
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118 chain = "--chain"
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119
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120 cmd = "lastz %s[format=fasta] %s[format=fasta] --output=%s --format=%s %s %s --step=%i %s %s" % (self.refFileName, self.queryFileName, self.outputFileName
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121 , self.outputFileFormat, ambiguous, transition,self.step, gfextend, chain)
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122 if self.verbosity>0:
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123 print("Running LastZ with following commands : %s" %cmd)
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124 sys.stdout.flush()
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125 cmd = cmd.split()
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126 process = subprocess.Popen(cmd)
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127 process.wait()
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128 return process.returncode
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129
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130 if __name__ == "__main__":
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131 iLaunchLastZ = LaunchLastZ()
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132 iLaunchLastZ.setAttributesFromCmdLine()
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133 iLaunchLastZ.run()
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