annotate commons/launcher/LaunchRefAlign.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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# "http://www.cecill.info". 
#
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from commons.core.LoggerFactory import LoggerFactory
from commons.core.utils.RepetOptionParser import RepetOptionParser
from commons.core.checker.ConfigChecker import ConfigRules
from commons.core.checker.ConfigChecker import ConfigChecker
import subprocess
import os
from commons.core.seq.Bioseq import Bioseq

LOG_DEPTH = "repet.core.launchers"

from commons.core.seq.BioseqDB import BioseqDB
from commons.tools.ChangeSequenceHeaders import ChangeSequenceHeaders


class LaunchRefAlign(object):
    """
    Launch 'refalign' to build a master-slave multiple sequence alignment.
    """
    def __init__(self, inputFileName="", outFileName="", gapSize=10, match=10, mismatch=8, gapOpen=16, gapExtend=4, refseqName="", keepRefseq =False, verbosity=3 ):
        self.inputFileName = inputFileName
        self.outFileName=outFileName
        self.gapSize = gapSize
        self.match = match
        self.mismatch = mismatch
        self.gapOpen = gapOpen
        self.gapExtend = gapExtend
        self.gapExtend = gapExtend
        self.refseqName = refseqName
        self.keepRefseq = keepRefseq
        self._verbosity = verbosity
        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
        
    def setAttributesFromCmdLine(self):
        description = "usage: LaunchRefalign.py [ options ]"
        epilog = "\n -h: this help\n"
        epilog += "\t -i: name of the input file (refseq is first, format='fasta')"
        epilog += "\t -r: keep the reference sequence"
        epilog += "\t -o: name of the output file (default=inFileName+'.fa_aln')"
        epilog += "\t -v: verbosity (default=0)"
        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("-r", "--keepRefseq", dest = "keepRefseq",    action = "store_true",                   help = "keep reference sequence [optional] [default: False]", default = False)
        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.keepRefseq = options.keepRefseq
        self._verbosity = options.verbosity

    def _checkOptions(self):
        if self.inputFileName == "":
            self._logAndRaise("ERROR: Missing input file name")
    
        if self.outFileName == "":
            self.outFileName = "%s.fa_aln" % (self.inputFileName)
            
    def _logAndRaise(self, errorMsg):
        self._log.error(errorMsg)
        raise Exception(errorMsg)
         
    def _prepareRefAlign(self):
        self.shortInputFileName = self.inputFileName+".shortH" 
        self.refFileName= self.shortInputFileName + ".ref"
        self.cpyFileName=self.shortInputFileName + ".cpy"
        
        file_db = open(self.shortInputFileName)
        file_ref = open(self.refFileName,"w")
        file_cpy = open(self.cpyFileName,"w")
        
        self._numseq=0
        while 1:
            seq=Bioseq()
            seq.read(file_db)
            if seq.sequence==None:
                break
            self._numseq+=1
            if self._numseq==1:
                seq.write(file_ref)
            else:
                seq.write(file_cpy)
        file_db.close()
        file_ref.close()
        file_cpy.close()
    
    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()
        
        bsDB = BioseqDB(self.inputFileName+".shortH")
        bsDB.upCase()
        bsDB.save(self.inputFileName+".shortHtmp")
        del bsDB
        os.rename(self.inputFileName+".shortHtmp", self.inputFileName+".shortH")
        
    def _renameHeaders(self):
        self.csh.setInputFile(self.inputFileName+".shortH.fa_aln")
        self.csh.setFormat("fasta")
        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 LaunchRefAlign")
        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()
        if self.keepRefseq:
            self.refseqName="seq1"
        self._prepareRefAlign()
        
        if self._numseq > 1:
            cmd = "refalign %s %s -m %d -l %d -d %d -g %d -e %d" % (self.refFileName, self.cpyFileName, self.match, self.gapSize, self.mismatch, self.gapOpen, self.gapExtend)
            
            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)
            refseqNameParam = ""
            if self.refseqName != "":
                refseqNameParam = "-r %s " % (self.refseqName)
            outFileName = self.inputFileName+".shortH.fa_aln"
            #self.cpyFileName = os.path.join(os.getcwd(),os.path.basename(self.cpyFileName))
            
            self._log.info("Copy file path %s " % self.cpyFileName)
            print("Copy file path %s " % self.cpyFileName)
            cmd = "refalign2fasta.py -i %s.aligner %s-g d -o %s -v 1" % (self.cpyFileName, refseqNameParam, outFileName)
            self._log.debug("Running : %s" % cmd)
            process = subprocess.Popen(cmd.split(' '), stdout=subprocess.PIPE, stderr=subprocess.PIPE)
            output = process.communicate()
            self._log.debug("Output:\n%s" % output[0])
            
            if process.returncode != 0:
                self._logAndRaise("ERROR when launching '%s'" % cmd)
                
            cmd = "rm -f "+ self.refFileName + " " + self.cpyFileName + " " + self.cpyFileName + ".aligner " + self.cpyFileName + ".oriented " + self.cpyFileName + ".refalign.stat"
            os.system(cmd)
            
        else:
            self._logAndRaise("Only one sequence available")
            cmd = "echo empty"
            
        self._renameHeaders()
        
        for fileName in [self.inputFileName + ".shortH", self.inputFileName + ".shortHlink", self.inputFileName + ".shortH.fa_aln"]:
            os.remove(fileName)
        self._log.info("END LaunchRefAlign")
        return 0
        

if __name__ == "__main__":
    iLaunchRefAlign = LaunchRefAlign()
    iLaunchRefAlign.setAttributesFromCmdLine()
    iLaunchRefAlign.run()