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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
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40 LOG_DEPTH = "repet.tools"
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41
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42 class LaunchNucmer(object):
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43
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44 def __init__(self,queryFileName="", refFileName ="", prefix = None, genCoords=False, showCoords = False, mum=False, maxGaps=90, minMatch=20, nooptimize=False,mincluster=65, minIdentity=50, minLength=100, verbosity=0):
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45 self._queryFileName = queryFileName
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46 self._refFileName = refFileName
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47 self._prefix = prefix
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48 self._genCoords = genCoords
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49 self._showCoords = showCoords
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50 self._mum = mum
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51 self._maxgaps = maxGaps
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52 self._minMatch = minMatch
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53 self._nooptimize = nooptimize
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54 self._mincluster = mincluster
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55 self._minIdentity = minIdentity
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56 self._minLength = minLength
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57 self.verbosity = verbosity
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58 self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self.verbosity)
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59
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60 def setMincluster(self, value):
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61 self._mincluster = value
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62 def getMincluster(self):
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63 return self._mincluster
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64
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65 mincluster = property(getMincluster, setMincluster)
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66
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67 def setAttributesFromCmdLine(self):
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68 description = "LaunchNucmer runs the Nucmer program (part of the mummer package) ."
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69 parser = RepetOptionParser(description = description)
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70 parser.add_option("-q", "--query", dest="queryFileName", default = "", action="store", type="string", help="input query file [compulsory] [format: fasta]")
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71 parser.add_option("-r", "--ref", dest="refFileName", default = "", action="store", type="string", help="input ref file [compulsory] [format: fasta]")
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72 parser.add_option("-p", "--prefix", dest="prefix", default = None, action="store", type="string", help="prefix name [optional]")
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73 parser.add_option("-o","--gencoords", dest="genCoords",action="store_true", help="generate coords file with minimal option (show-coords -r) [optional] ")
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74 parser.add_option("-s","--showcoords", dest="showCoords",action="store_true", help="generate coords file with: show-coords -r -c -l -d -I 50 -L 100 -T [optional] ")
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75 parser.add_option("-m", "--mum", dest="mum", action="store_true", help="Use anchor matches that are unique in both the reference and query [optional] ")
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76 parser.add_option("-g", "--maxgaps", dest="maxgaps", default = 90, action="store", type="int", help="Maximum gap between two adjacent matches in a cluster (default 90) [optional] ")
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77 parser.add_option("-l", "--minmatch", dest="minMatch", default = 20, action="store", type="int", help="Minimum length of an maximal exact match (default 20) [optional] ")
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78 parser.add_option("-n", "--nooptimize", dest="nooptimize", action="store_true", help="nooptimize (default --optimize) [optional] ")
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79 parser.add_option("-j", "--mincluster", dest="mincluster", default = 65, action="store", type="int", help="Minimum length of a cluster of matches (default 65) [optional] ")
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80
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81 parser.add_option("-i", "--minIdentity", dest="minIdentity", default = 50, action="store", type="int", help="Minimum identity for show_coords (default 50) [optional] ")
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82 parser.add_option("-u", "--minLength", dest="minLength", default = 100, action="store", type="int", help="Minimum alignment length for show_coords (default 100) [optional] ")
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83 parser.add_option("-v", "--verbosity", dest="verbosity", default = 0, action="store", type="int", help="verbosity [optional] ")
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84
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85 (self._options, args) = parser.parse_args()
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86 self._setAttributesFromOptions(self._options)
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87
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88 def _setAttributesFromOptions(self, options):
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89 self._queryFileName = options.queryFileName
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90 self._refFileName = options.refFileName
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91 self._prefix = options.prefix
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92 self._genCoords = options.genCoords
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93 self._showCoords = options.showCoords
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94 self._mum = options.mum
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95 self._maxgaps = options.maxgaps
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96 self._minMatch = options.minMatch
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97 self._nooptimize = options.nooptimize
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98 self._mincluster = options.mincluster
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99
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100 self._minIdentity = options.minIdentity
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101 self._minLength = options.minLength
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102
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103 self.verbosity = options.verbosity
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104
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105 def _logAndRaise(self, errorMsg):
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106 self._log.error(errorMsg)
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107 raise Exception(errorMsg)
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108
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109 def checkOptions(self):
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110 if self._queryFileName != "":
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111 if not FileUtils.isRessourceExists(self._queryFileName):
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112 self._logAndRaise("ERROR: Query file: %s does not exist!" % self._queryFileName)
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113 else:
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114 self._logAndRaise("ERROR: No specified --query option!")
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115
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116 if self._refFileName != "":
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117 if not FileUtils.isRessourceExists(self._refFileName):
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118 self._logAndRaise("ERROR: Ref file does not exist!"% self._refFileName)
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119 else:
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120 self._logAndRaise("ERROR: No specified --ref option!")
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121
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122 def run(self):
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123 LoggerFactory.setLevel(self._log, self.verbosity)
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124 if not CheckerUtils.isExecutableInUserPath("nucmer") :
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125 self._logAndRaise("ERROR: nucmer must be in your path")
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126 self.checkOptions()
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127
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128 genCoords = ""
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129 if self._genCoords:
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130 genCoords = "-o"
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131 mum = ""
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132 if self._mum:
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133 mum = "--mum"
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134 nooptimize = "--optimize"
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135 if self._nooptimize:
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136 nooptimize = "--nooptimize"
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137 prefix = ""
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138 if self._prefix is not None:
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139 prefix = "--prefix=%s" %(self._prefix)
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140 cmd = "nucmer %s %s %s %s %s -g=%d -l=%d %s -c=%d" % (self._refFileName,self._queryFileName, prefix, genCoords, mum, self._maxgaps, self._minMatch, nooptimize, self._mincluster)
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141 self._log.debug("Running nucmer with following commands : %s" %cmd)
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142 cmd = cmd.split()
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143 process = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
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144 process.wait()
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145
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146 if self._showCoords:
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147 #use of os.system because redirect on process is broken in python < 3.0
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148 cmd = "show-coords -r -c -l -d -I %d -L %d -T %s.delta > %s.coords" % (self._minIdentity, self._minLength, self._prefix, self._prefix)
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149 self._log.debug("Running show-coords with following commands : %s" %cmd)
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150 os.system(cmd)
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151
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152
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153 return process.returncode
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154
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155 if __name__ == "__main__":
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156 iLaunchNucmer = LaunchNucmer()
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157 iLaunchNucmer.setAttributesFromCmdLine()
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158 iLaunchNucmer.run() |
