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comparison commons/launcher/LaunchPhyML.py @ 31:0ab839023fe4

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author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
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30:5677346472b5 31:0ab839023fe4
1 #!/usr/bin/env python
2
3 # Copyright INRA (Institut National de la Recherche Agronomique)
4 # http://www.inra.fr
5 # http://urgi.versailles.inra.fr
6 #
7 # This software is governed by the CeCILL license under French law and
8 # abiding by the rules of distribution of free software. You can use,
9 # modify and/ or redistribute the software under the terms of the CeCILL
10 # license as circulated by CEA, CNRS and INRIA at the following URL
11 # "http://www.cecill.info".
12 #
13 # As a counterpart to the access to the source code and rights to copy,
14 # modify and redistribute granted by the license, users are provided only
15 # with a limited warranty and the software's author, the holder of the
16 # economic rights, and the successive licensors have only limited
17 # liability.
18 #
19 # In this respect, the user's attention is drawn to the risks associated
20 # with loading, using, modifying and/or developing or reproducing the
21 # software by the user in light of its specific status of free software,
22 # that may mean that it is complicated to manipulate, and that also
23 # therefore means that it is reserved for developers and experienced
24 # professionals having in-depth computer knowledge. Users are therefore
25 # encouraged to load and test the software's suitability as regards their
26 # requirements in conditions enabling the security of their systems and/or
27 # data to be ensured and, more generally, to use and operate it in the
28 # same conditions as regards security.
29 #
30 # The fact that you are presently reading this means that you have had
31 # knowledge of the CeCILL license and that you accept its terms.
32
33 from commons.core.LoggerFactory import LoggerFactory
34 from commons.core.utils.RepetOptionParser import RepetOptionParser
35 from commons.tools.ChangeSequenceHeaders import ChangeSequenceHeaders
36 import subprocess
37 import os
38 from commons.core.seq.Bioseq import Bioseq
39 import shutil
40
41 LOG_DEPTH = "repet.core.launchers"
42
43
44
45 class LaunchPhyML(object):
46 """
47 Launch 'PhyML'
48 """
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 ):
50 self.inputFileName = inputFileName
51 self.outFileName=outFileName
52 self.dataType = dataType #"nt or aa"
53 self._setSeqFormat(interleavedFormat) #if False -q"
54 self.nbDataSets = nbDataSets
55 self.nbBootDataSets = nbBootDataSets
56 self.substModel = substModel
57 self.ratioTsTv = ratioTsTv
58 self.propInvSites = propInvSites # propInvSites="e" replaced by 0.0; should be in [0-1]
59 self.nbCat = nbCat # Number of categories less than four or higher than eight are not recommended.
60 self.gammaParam = gammaParam
61 self.startTree = startTree #by default is BIONJ used reformatedInputFileName+"_phyml_tree.txt" instead
62 self.paramOptimisation = paramOptimisation # used instead of self.optTopology="y", self.optBranchRate="y"
63 #This option focuses on specific parameter optimisation.
64 #tlr : tree topology (t), branch length (l) and rate parameters (r) are optimised.
65 #tl : tree topology and branch length are optimised.
66 #lr : branch length and rate parameters are optimised.
67 #l : branch length are optimised.
68 #r : rate parameters are optimised.
69 #n : no parameter is optimised.
70
71 self._clean = clean
72 self._verbosity = verbosity
73 self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
74
75 def _setSeqFormat(self, interleavedFormat):
76 if not (interleavedFormat) :
77 self.seqFormat = " -q"
78 else :
79 self.seqFormat = ""
80
81 def setAttributesFromCmdLine(self):
82 description = "usage: LaunchPhyML.py [ options ]"
83 epilog = "\n -h: this help\n"
84 epilog += "\t -i: name of the input file (refseq is first, format='fasta')"
85 epilog += "\n\t"
86 parser = RepetOptionParser(description = description, epilog = epilog)
87 parser.add_option("-i", "--fasta", dest = "inputFileName", action = "store", type = "string", help = "input fasta file name [compulsory] [format: fasta]", default = "")
88 parser.add_option("-o", "--out", dest = "outFileName", action = "store", type = "string", help = "output file name [default: <input>.out]", default = "")
89 parser.add_option("-v", "--verbosity", dest = "verbosity", action = "store", type = "int", help = "verbosity [optional] [default: 1]", default = 1)
90 options = parser.parse_args()[0]
91 self._setAttributesFromOptions(options)
92
93 def _setAttributesFromOptions(self, options):
94 self.inputFileName = options.inputFileName
95 self.setOutFileName = options.outFileName
96 self._verbosity = options.verbosity
97
98 def _checkOptions(self):
99 if self.inputFileName == "":
100 self._logAndRaise("ERROR: Missing input file name")
101
102 if self.outFileName == "":
103 self.outFileName = "%s_phyml.newick" % (self.inputFileName)
104
105 def _logAndRaise(self, errorMsg):
106 self._log.error(errorMsg)
107 raise Exception(errorMsg)
108
109 def _shortenHeaders(self):
110 self.csh = ChangeSequenceHeaders()
111 self.csh.setInputFile(self.inputFileName)
112 self.csh.setFormat("fasta")
113 self.csh.setStep(1)
114 self.csh.setPrefix("seq")
115 self.csh.setLinkFile(self.inputFileName+".shortHlink")
116 self.csh.setOutputFile(self.inputFileName+".shortH")
117 self.csh.setVerbosityLevel(self._verbosity-1)
118 self.csh.run()
119 self.shortInputFileName = self.inputFileName+".shortH"
120
121 def _renameHeaders(self):
122 self.csh.setInputFile(self.phyml_tree)
123 self.csh.setFormat("newick")
124 self.csh.setStep(2)
125 self.csh.setLinkFile(self.inputFileName+".shortHlink" )
126 self.csh.setOutputFile(self.outFileName)
127 self.csh.setVerbosityLevel(self._verbosity-1)
128 self.csh.run()
129
130 def run(self):
131 LoggerFactory.setLevel(self._log, self._verbosity)
132 self._checkOptions()
133 self._log.info("START LaunchPhyML")
134 self._log.debug("building a multiple alignment from '%s'..." % ( self.inputFileName))
135
136 inputFileName = "%s/%s" % (os.getcwd(), os.path.basename(self.inputFileName))
137 if not os.path.exists(inputFileName):
138 os.symlink(self.inputFileName, inputFileName)
139 self.inputFileName = inputFileName
140
141 self._shortenHeaders()
142
143 cmd = "sreformat phylip %s" % (self.shortInputFileName)
144
145 with open (self.reformatedInputFileName, "w") as fPhylip :
146
147 process = subprocess.Popen(cmd.split(' '), stdout= fPhylip , stderr=subprocess.PIPE)
148 self._log.debug("Running : %s" % cmd)
149 output = process.communicate()
150 self._log.debug("Output:\n%s" % output[0])
151 if process.returncode != 0:
152 self._logAndRaise("ERROR when launching '%s'" % cmd)
153
154 self.reformatedInputFileName = "%s.phylip" % self.shortInputFileName
155 self.phyml_tree = "%s_phyml_tree.txt" %self.reformatedInputFileName
156 cpyPhyml_tree = "%s_cpy" %self.phyml_tree
157 shutil.copyfile(self.phyml_tree,cpyPhyml_tree)
158
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 )
160 print cmd
161 process = subprocess.Popen(cmd.split(' '), stdout=subprocess.PIPE, stderr=subprocess.PIPE)
162 self._log.debug("Running : %s" % cmd)
163 output = process.communicate()
164 self._log.debug("Output:\n%s" % output[0])
165 if process.returncode != 0:
166 self._logAndRaise("ERROR when launching '%s'" % cmd)
167
168 self._renameHeaders()
169
170 if self._clean:
171 for f in [ self.shortInputFileName, self.inputFileName+".shortHlink", self.inputFileName+".shortH.phylip",self.inputFileName+".shortH.phylip_phyml_lk.txt", self.phyml_tree ]:
172 os.remove(f)
173 os.system( "mv %s.phylip_phyml_stat.txt %s_phyml.txt" % ( self.shortInputFileName, self.inputFileName ) )
174
175 self._log.info("Finished running LaunchPhyML")
176
177