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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.LoggerFactory import LoggerFactory
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34 from commons.core.utils.RepetOptionParser import RepetOptionParser
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35 from commons.core.seq.AlignedBioseqDB import AlignedBioseqDB
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36 from commons.core.seq.FastaUtils import FastaUtils
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37 from commons.tools.ChangeSequenceHeaders import ChangeSequenceHeaders
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38 from commons.core.utils.FileUtils import FileUtils
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39 import os
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40 import subprocess
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41
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42 LOG_DEPTH = "repet.tools"
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43
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44 ##Reference launcher implementation
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45 #
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46 class LaunchMap(object):
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47
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48 def __init__(self, fastaFileName = "", outFileName = "", gapSize = 50, mismatchPenalty = -8, gapOpenPenalty = 16, gapExtendPenalty = 4, doClean = False, verbosity = 0):
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49 self._fastaFileName = fastaFileName
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50 self.setOutFileName(outFileName)
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51 self._gapSize = gapSize
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52 self._mismatchPenalty = mismatchPenalty
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53 self._gapOpenPenalty = gapOpenPenalty
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54 self._gapExtendPenalty = gapExtendPenalty
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55 self._doClean = doClean
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56 self._verbosity = verbosity
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57 self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
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58
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59 def setAttributesFromCmdLine(self):
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60 # description = "Launch template to create a launcher."
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61 # epilog = "\nExample 1: launch without verbosity and keep temporary files.\n"
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62 # epilog += "\t$ python LaunchTemplate.py -i file.fa -v 0"
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63 # epilog += "\n\t"
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64 # epilog += "\nExample 2: launch with verbosity to have errors (level 1) and basic information (level 2), and delete temporary files.\n"
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65 # epilog += "\t$ python LaunchTemplate.py -i file.fa -c -v 2"
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66 # parser = RepetOptionParser(description = description, epilog = epilog)
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67 parser = RepetOptionParser(description = "", epilog = "")
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68 parser.add_option("-i", "--fasta", dest = "fastaFileName", action = "store", type = "string", help = "input fasta file name [compulsory] [format: fasta]", default = "")
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69 parser.add_option("-o", "--out", dest = "outFileName", action = "store", type = "string", help = "output file name [default: <input>.fa_aln]", default = "")
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70 parser.add_option("-s", "--gapSize", dest = "gapSize", action = "store", type = "int", help = "size above which a gap is not penalized anymore [optional] [default: 50]", default = 50)
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71 parser.add_option("-m", "--mismatch", dest = "mismatch", action = "store", type = "int", help = "penalty for a mismatch [optional] [default: -8]", default = -8)
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72 parser.add_option("-O", "--gapOpen", dest = "gapOpen", action = "store", type = "int", help = "penalty for a gap opening [optional] [default: 16]", default = 16)
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73 parser.add_option("-e", "--gapExtend", dest = "gapExtend", action = "store", type = "int", help = "penalty for a gap extension [optional] [default: 4]", default = 4)
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74 parser.add_option("-c", "--clean", dest = "doClean", action = "store_true", help = "clean temporary files [optional] [default: False]", default = False)
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75 parser.add_option("-v", "--verbosity", dest = "verbosity", action = "store", type = "int", help = "verbosity [optional] [default: 1]", default = 1)
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76 options = parser.parse_args()[0]
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77 self._setAttributesFromOptions(options)
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78
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79 def _setAttributesFromOptions(self, options):
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80 self.setFastaFileName(options.fastaFileName)
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81 self.setOutFileName(options.outFileName)
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82 self.setGapSize(options.gapSize)
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83 self.setMismatchPenalty(options.mismatch)
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84 self.setGapOpenPenalty(options.gapOpen)
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85 self.setGapExtendPenalty(options.gapExtend)
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86 self.setDoClean(options.doClean)
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87 self.setVerbosity(options.verbosity)
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88
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89 def setFastaFileName(self, fastaFileName):
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90 self._fastaFileName = fastaFileName
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91
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92 def setOutFileName(self, outFileName):
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93 if outFileName == "":
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94 self._outFileName = "%s.fa_aln" % self._fastaFileName
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95 else:
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96 self._outFileName = outFileName
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97
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98 def setGapSize(self, gapSize):
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99 self._gapSize = gapSize
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100
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101 def setMismatchPenalty(self, mismatchPenalty):
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102 self._mismatchPenalty = mismatchPenalty
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103
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104 def setGapOpenPenalty(self, gapOpenPenalty):
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105 self._gapOpenPenalty = gapOpenPenalty
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106
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107 def setGapExtendPenalty(self, gapExtendPenalty):
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108 self._gapExtendPenalty = gapExtendPenalty
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109
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110 def setDoClean(self, doClean):
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111 self._doClean = doClean
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112
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113 def setVerbosity(self, verbosity):
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114 self._verbosity = verbosity
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115
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116 def _checkOptions(self):
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117 if self._fastaFileName == "":
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118 self._logAndRaise("ERROR: Missing input fasta file name")
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119 if not FileUtils.isRessourceExists(self._fastaFileName):
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120 self._logAndRaise("ERROR: Input fasta file name %s doesn't exist." % self._fastaFileName)
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121
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122 def _logAndRaise(self, errorMsg):
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123 self._log.error(errorMsg)
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124 raise Exception(errorMsg)
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125
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126 def getMapCmd(self):
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127 cmd = "rpt_map"
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128 cmd += " %s.shortH" % self._fastaFileName
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129 cmd += " %i" % self._gapSize
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130 cmd += " %i" % self._mismatchPenalty
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131 cmd += " %i" % self._gapOpenPenalty
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132 cmd += " %i" % self._gapExtendPenalty
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133 cmd += " > %s.shortH.fa_aln" % self._fastaFileName
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134 return cmd
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135
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136 def run(self):
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137 LoggerFactory.setLevel(self._log, self._verbosity)
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138 self._checkOptions()
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139 self._log.info("START LaunchMap")
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140 self._log.debug("Fasta file name: %s" % self._fastaFileName)
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141
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142 lInitHeaders = FastaUtils.dbHeaders(self._fastaFileName, self._verbosity - 1)
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143
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144 csh = ChangeSequenceHeaders()
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145 csh.setInputFile(self._fastaFileName)
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146 csh.setFormat("fasta")
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147 csh.setStep(1)
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148 csh.setPrefix("seq")
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149 csh.setLinkFile("%s.shortHlink" % self._fastaFileName)
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150 csh.setOutputFile("%s.shortH" % self._fastaFileName)
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151 csh.setVerbosityLevel(self._verbosity - 1)
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152 csh.run()
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153
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154 cmd = self.getMapCmd()
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155 process = subprocess.Popen(cmd, shell = True)
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156 self._log.debug("Running : %s" % cmd)
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157 process.communicate()
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158 if process.returncode != 0:
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159 self._logAndRaise("ERROR when launching '%s'" % cmd)
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160
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161 csh.setInputFile("%s.shortH.fa_aln" % self._fastaFileName)
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162 csh.setFormat("fasta")
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163 csh.setStep(2)
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164 csh.setLinkFile("%s.shortHlink" % self._fastaFileName)
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165 csh.setOutputFile("%s.shortH.fa_aln.initH" % self._fastaFileName)
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166 csh.setVerbosityLevel(self._verbosity - 1)
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167 csh.run()
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168
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169 absDB = AlignedBioseqDB("%s.shortH.fa_aln.initH" % self._fastaFileName)
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170 outFileHandler = open(self._outFileName, "w")
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171 for header in lInitHeaders:
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172 bs = absDB.fetch(header)
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173 bs.upCase()
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174 bs.write(outFileHandler)
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175 outFileHandler.close()
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176 if self._doClean:
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177 os.remove("%s.shortH" % self._fastaFileName)
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178 os.remove("%s.shortHlink" % self._fastaFileName)
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179 os.remove("%s.shortH.fa_aln" % self._fastaFileName)
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180 os.remove("%s.shortH.fa_aln.initH" % self._fastaFileName)
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181 self._log.info("END Launch")
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182
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183 if __name__ == "__main__":
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184 iLaunch = LaunchMap()
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185 iLaunch.setAttributesFromCmdLine()
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186 iLaunch.run() |
