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

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#!/usr/bin/env python

# Copyright INRA (Institut National de la Recherche Agronomique)
# http://www.inra.fr
# http://urgi.versailles.inra.fr
#
# This software is governed by the CeCILL license under French law and
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# modify and/ or redistribute the software under the terms of the CeCILL
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from commons.core.LoggerFactory import LoggerFactory
from commons.core.utils.RepetOptionParser import RepetOptionParser
from commons.tools.ChangeSequenceHeaders import ChangeSequenceHeaders
import subprocess
import os
from commons.core.seq.Bioseq import Bioseq
import shutil

LOG_DEPTH = "repet.core.launchers"



class LaunchPhyML(object):
    """
    Launch 'PhyML'
    """
    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 ):
        self.inputFileName = inputFileName
        self.outFileName=outFileName
        self.dataType = dataType                    #"nt or aa"
        self._setSeqFormat(interleavedFormat)       #if False -q"
        self.nbDataSets = nbDataSets
        self.nbBootDataSets = nbBootDataSets
        self.substModel = substModel
        self.ratioTsTv = ratioTsTv
        self.propInvSites = propInvSites            # propInvSites="e" replaced by 0.0; should be in [0-1]
        self.nbCat = nbCat                          # Number of categories less than four or higher than eight are not recommended.
        self.gammaParam = gammaParam
        self.startTree = startTree                  #by default is BIONJ used reformatedInputFileName+"_phyml_tree.txt" instead
        self.paramOptimisation = paramOptimisation  # used instead of self.optTopology="y", self.optBranchRate="y" 
                                                    #This option focuses on specific parameter optimisation.
                                                    #tlr : tree topology (t), branch length (l) and rate parameters (r) are optimised.
                                                    #tl  : tree topology and branch length are optimised.
                                                    #lr  : branch length and rate parameters are optimised.
                                                    #l   : branch length are optimised.
                                                    #r   : rate parameters are optimised.
                                                    #n   : no parameter is optimised.

        self._clean = clean
        self._verbosity = verbosity
        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
    
    def _setSeqFormat(self, interleavedFormat):
        if not (interleavedFormat) :
            self.seqFormat = " -q"
        else :
            self.seqFormat = ""
            
    def setAttributesFromCmdLine(self):
        description = "usage: LaunchPhyML.py [ options ]"
        epilog = "\n -h: this help\n"
        epilog += "\t -i: name of the input file (refseq is first, format='fasta')"
        epilog += "\n\t"
        parser = RepetOptionParser(description = description, epilog = epilog)
        parser.add_option("-i", "--fasta",      dest = "inputFileName", action = "store",       type = "string", help = "input fasta file name [compulsory] [format: fasta]", default = "")
        parser.add_option("-o", "--out",        dest = "outFileName",   action = "store",       type = "string", help = "output file name [default: <input>.out]", default = "")
        parser.add_option("-v", "--verbosity",  dest = "verbosity",     action = "store",       type = "int",    help = "verbosity [optional] [default: 1]", default = 1)
        options = parser.parse_args()[0]
        self._setAttributesFromOptions(options)
        
    def _setAttributesFromOptions(self, options):
        self.inputFileName = options.inputFileName
        self.setOutFileName = options.outFileName
        self._verbosity = options.verbosity

    def _checkOptions(self):
        if self.inputFileName == "":
            self._logAndRaise("ERROR: Missing input file name")
    
        if self.outFileName == "":
            self.outFileName = "%s_phyml.newick" % (self.inputFileName)
            
    def _logAndRaise(self, errorMsg):
        self._log.error(errorMsg)
        raise Exception(errorMsg)
         
    def _shortenHeaders(self):
        self.csh = ChangeSequenceHeaders()
        self.csh.setInputFile(self.inputFileName)
        self.csh.setFormat("fasta")
        self.csh.setStep(1)
        self.csh.setPrefix("seq")
        self.csh.setLinkFile(self.inputFileName+".shortHlink")
        self.csh.setOutputFile(self.inputFileName+".shortH")
        self.csh.setVerbosityLevel(self._verbosity-1)
        self.csh.run()
        self.shortInputFileName = self.inputFileName+".shortH" 
        
    def _renameHeaders(self):
        self.csh.setInputFile(self.phyml_tree)
        self.csh.setFormat("newick")
        self.csh.setStep(2)
        self.csh.setLinkFile(self.inputFileName+".shortHlink" )
        self.csh.setOutputFile(self.outFileName)
        self.csh.setVerbosityLevel(self._verbosity-1)
        self.csh.run()
          
    def run(self):
        LoggerFactory.setLevel(self._log, self._verbosity)
        self._checkOptions()
        self._log.info("START LaunchPhyML")
        self._log.debug("building a multiple alignment from '%s'..." % ( self.inputFileName))
        
        inputFileName = "%s/%s" % (os.getcwd(), os.path.basename(self.inputFileName))
        if not os.path.exists(inputFileName):
            os.symlink(self.inputFileName, inputFileName)
        self.inputFileName = inputFileName
        
        self._shortenHeaders()

        cmd = "sreformat phylip %s" % (self.shortInputFileName)
        
        with open (self.reformatedInputFileName, "w") as fPhylip :
            
            process = subprocess.Popen(cmd.split(' '), stdout= fPhylip , stderr=subprocess.PIPE)
            self._log.debug("Running : %s" % cmd)
            output = process.communicate()
            self._log.debug("Output:\n%s" % output[0])
            if process.returncode != 0:
                self._logAndRaise("ERROR when launching '%s'" % cmd)
        
        self.reformatedInputFileName = "%s.phylip" % self.shortInputFileName
        self.phyml_tree = "%s_phyml_tree.txt" %self.reformatedInputFileName 
        cpyPhyml_tree = "%s_cpy" %self.phyml_tree
        shutil.copyfile(self.phyml_tree,cpyPhyml_tree)
                          
        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 )
        print cmd    
        process = subprocess.Popen(cmd.split(' '), stdout=subprocess.PIPE, stderr=subprocess.PIPE)
        self._log.debug("Running : %s" % cmd)
        output = process.communicate()
        self._log.debug("Output:\n%s" % output[0])
        if process.returncode != 0:
            self._logAndRaise("ERROR when launching '%s'" % cmd)
        
        self._renameHeaders()
        
        if self._clean:
            for f in [ self.shortInputFileName, self.inputFileName+".shortHlink", self.inputFileName+".shortH.phylip",self.inputFileName+".shortH.phylip_phyml_lk.txt", self.phyml_tree ]:
                os.remove(f)
            os.system( "mv %s.phylip_phyml_stat.txt %s_phyml.txt" % ( self.shortInputFileName, self.inputFileName ) )
        
        self._log.info("Finished running LaunchPhyML")