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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.tools.ChangeSequenceHeaders import ChangeSequenceHeaders
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36 import subprocess
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37 import os
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38 from commons.core.seq.Bioseq import Bioseq
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39 import shutil
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40
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41 LOG_DEPTH = "repet.core.launchers"
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42
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43
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44
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45 class LaunchPhyML(object):
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46 """
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47 Launch 'PhyML'
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48 """
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49 def __init__(self, inputFileName="", outFileName="",dataType= "nt", interleavedFormat= True, nbDataSets=1, nbBootDataSets=0, substModel="HKY85", ratioTsTv=4.0, propInvSites= 0.0, nbCat=1, gammaParam=1.0, startTree="BIONJ", paramOptimisation = "tlr", clean=False, verbosity=3 ):
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50 self.inputFileName = inputFileName
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51 self.outFileName=outFileName
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52 self.dataType = dataType #"nt or aa"
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53 self._setSeqFormat(interleavedFormat) #if False -q"
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54 self.nbDataSets = nbDataSets
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55 self.nbBootDataSets = nbBootDataSets
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56 self.substModel = substModel
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57 self.ratioTsTv = ratioTsTv
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58 self.propInvSites = propInvSites # propInvSites="e" replaced by 0.0; should be in [0-1]
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59 self.nbCat = nbCat # Number of categories less than four or higher than eight are not recommended.
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60 self.gammaParam = gammaParam
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61 self.startTree = startTree #by default is BIONJ used reformatedInputFileName+"_phyml_tree.txt" instead
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62 self.paramOptimisation = paramOptimisation # used instead of self.optTopology="y", self.optBranchRate="y"
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63 #This option focuses on specific parameter optimisation.
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64 #tlr : tree topology (t), branch length (l) and rate parameters (r) are optimised.
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65 #tl : tree topology and branch length are optimised.
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66 #lr : branch length and rate parameters are optimised.
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67 #l : branch length are optimised.
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68 #r : rate parameters are optimised.
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69 #n : no parameter is optimised.
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70
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71 self._clean = clean
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72 self._verbosity = verbosity
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73 self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
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74
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75 def _setSeqFormat(self, interleavedFormat):
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76 if not (interleavedFormat) :
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77 self.seqFormat = " -q"
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78 else :
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79 self.seqFormat = ""
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80
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81 def setAttributesFromCmdLine(self):
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82 description = "usage: LaunchPhyML.py [ options ]"
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83 epilog = "\n -h: this help\n"
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84 epilog += "\t -i: name of the input file (refseq is first, format='fasta')"
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85 epilog += "\n\t"
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86 parser = RepetOptionParser(description = description, epilog = epilog)
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87 parser.add_option("-i", "--fasta", dest = "inputFileName", action = "store", type = "string", help = "input fasta file name [compulsory] [format: fasta]", default = "")
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88 parser.add_option("-o", "--out", dest = "outFileName", action = "store", type = "string", help = "output file name [default: <input>.out]", default = "")
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89 parser.add_option("-v", "--verbosity", dest = "verbosity", action = "store", type = "int", help = "verbosity [optional] [default: 1]", default = 1)
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90 options = parser.parse_args()[0]
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91 self._setAttributesFromOptions(options)
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92
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93 def _setAttributesFromOptions(self, options):
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94 self.inputFileName = options.inputFileName
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95 self.setOutFileName = options.outFileName
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96 self._verbosity = options.verbosity
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97
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98 def _checkOptions(self):
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99 if self.inputFileName == "":
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100 self._logAndRaise("ERROR: Missing input file name")
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101
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102 if self.outFileName == "":
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103 self.outFileName = "%s_phyml.newick" % (self.inputFileName)
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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 _shortenHeaders(self):
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110 self.csh = ChangeSequenceHeaders()
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111 self.csh.setInputFile(self.inputFileName)
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112 self.csh.setFormat("fasta")
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113 self.csh.setStep(1)
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114 self.csh.setPrefix("seq")
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115 self.csh.setLinkFile(self.inputFileName+".shortHlink")
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116 self.csh.setOutputFile(self.inputFileName+".shortH")
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117 self.csh.setVerbosityLevel(self._verbosity-1)
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118 self.csh.run()
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119 self.shortInputFileName = self.inputFileName+".shortH"
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120
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121 def _renameHeaders(self):
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122 self.csh.setInputFile(self.phyml_tree)
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123 self.csh.setFormat("newick")
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124 self.csh.setStep(2)
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125 self.csh.setLinkFile(self.inputFileName+".shortHlink" )
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126 self.csh.setOutputFile(self.outFileName)
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127 self.csh.setVerbosityLevel(self._verbosity-1)
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128 self.csh.run()
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129
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130 def run(self):
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131 LoggerFactory.setLevel(self._log, self._verbosity)
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132 self._checkOptions()
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133 self._log.info("START LaunchPhyML")
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134 self._log.debug("building a multiple alignment from '%s'..." % ( self.inputFileName))
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135
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136 inputFileName = "%s/%s" % (os.getcwd(), os.path.basename(self.inputFileName))
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137 if not os.path.exists(inputFileName):
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138 os.symlink(self.inputFileName, inputFileName)
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139 self.inputFileName = inputFileName
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140
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141 self._shortenHeaders()
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142
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143 cmd = "sreformat phylip %s" % (self.shortInputFileName)
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144
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145 with open (self.reformatedInputFileName, "w") as fPhylip :
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146
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147 process = subprocess.Popen(cmd.split(' '), stdout= fPhylip , stderr=subprocess.PIPE)
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148 self._log.debug("Running : %s" % cmd)
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149 output = process.communicate()
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150 self._log.debug("Output:\n%s" % output[0])
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151 if process.returncode != 0:
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152 self._logAndRaise("ERROR when launching '%s'" % cmd)
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153
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154 self.reformatedInputFileName = "%s.phylip" % self.shortInputFileName
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155 self.phyml_tree = "%s_phyml_tree.txt" %self.reformatedInputFileName
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156 cpyPhyml_tree = "%s_cpy" %self.phyml_tree
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157 shutil.copyfile(self.phyml_tree,cpyPhyml_tree)
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158
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159 cmd = "phyml -i %s -d %s%s -n %d -b %d -m %s -t %f -v %f -c %d -a %f -u %s -o %s" % (self.reformatedInputFileName, self.dataType, self.seqFormat, self.nbDataSets,self.nbBootDataSets,self.substModel, self.ratioTsTv, self.propInvSites,self.nbCat,self.gammaParam, cpyPhyml_tree , self.paramOptimisation )
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160 print cmd
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161 process = subprocess.Popen(cmd.split(' '), stdout=subprocess.PIPE, stderr=subprocess.PIPE)
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162 self._log.debug("Running : %s" % cmd)
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163 output = process.communicate()
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164 self._log.debug("Output:\n%s" % output[0])
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165 if process.returncode != 0:
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166 self._logAndRaise("ERROR when launching '%s'" % cmd)
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167
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168 self._renameHeaders()
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169
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170 if self._clean:
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171 for f in [ self.shortInputFileName, self.inputFileName+".shortHlink", self.inputFileName+".shortH.phylip",self.inputFileName+".shortH.phylip_phyml_lk.txt", self.phyml_tree ]:
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172 os.remove(f)
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173 os.system( "mv %s.phylip_phyml_stat.txt %s_phyml.txt" % ( self.shortInputFileName, self.inputFileName ) )
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174
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175 self._log.info("Finished running LaunchPhyML")
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176
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177
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