def create(self, infile): """create profile library from file.""" self.mOutfileDatabase = open(self.mFilenameProfiles, "wb") outfile_index = open(self.mFilenameIndex, "w") ninput, noutput = 0, 0 while mali.readFromFile(sys.stdin, format="profile"): ninput += 1 m = Mali.convertMali2Alignlib(mali) p = alignlib_lite.py_makeProfile(m, weightor=self.mWeightor) p.prepare() self.appendProfile(mali.getName(), p) noutput += 1 return ninput, noutput
def create( self, infile ): """create profile library from file.""" self.mOutfileDatabase = open( self.mFilenameProfiles, "wb" ) outfile_index = open( self.mFilenameIndex, "w" ) ninput, noutput = 0, 0 while mali.readFromFile( sys.stdin, format="profile" ): ninput += 1 m = Mali.convertMali2Alignlib( mali ) p = alignlib_lite.py_makeProfile( m, weightor = self.mWeightor ) p.prepare() self.appendProfile( mali.getName(), p ) noutput += 1 return ninput, noutput
def verify( self, infile ): """verify data in database against original data.""" if not self.mIndex: self.__loadIndex() ninput, nfound, nnotfound, ndifferent = 0,0,0,0 while mali.readFromFile( sys.stdin, format="profile" ): ninput += 1 m = Mali.convertMali2Alignlib( mali ) p1 = alignlib_lite.py_makeProfile( m ) p1.prepare() p2 = self.getProfile( mali.getName() ) if p1.getLength() != p2.getLength() or \ str(p1) != str(p2): ndifferent += 1 continue nfound += 1 return ninput, nfound, nnotfound, ndifferent
def main(argv=None): """script main. parses command line options in sys.argv, unless *argv* is given. """ if not argv: argv = sys.argv # setup command line parser parser = E.OptionParser(version="%prog version: $Id: cgat_script_template.py 2871 2010-03-03 10:20:44Z andreas $", usage=globals()["__doc__"]) parser.add_option("-o", "--gop", dest="gop", type="float", help="gap opening penalty [default=%default].") parser.add_option("-e", "--gep", dest="gep", type="float", help="gap extension penalty [default=%default].") parser.add_option("-m", "--mode", dest="mode", type="choice", choices=("global", "local"), help="alignment mode, global=nw, local=sw [default=%default].") parser.set_defaults( gop=-12.0, gep=-2.0, format="fasta", mode="local", ) # add common options (-h/--help, ...) and parse command line (options, args) = E.Start(parser, argv=argv) if len(args) != 2: raise ValueError( "please supply two multiple alignments in FASTA format.") mali1 = Mali.Mali() mali2 = Mali.Mali() E.info("read 2 multiple alignments") mali1.readFromFile(IOTools.openFile(args[0], "r"), format=options.format) mali2.readFromFile(IOTools.openFile(args[1], "r"), format=options.format) cmali1 = Mali.convertMali2Alignlib(mali1) cmali2 = Mali.convertMali2Alignlib(mali2) if options.mode == "local": mode = alignlib_lite.py_ALIGNMENT_LOCAL elif options.mode == "global": mode = alignlib_lite.py_ALIGNMENT_GLOBAL alignator = alignlib_lite.py_makeAlignatorDPFull(mode, options.gop, options.gep) alignlib_lite.py_setDefaultEncoder( alignlib_lite.py_getEncoder(alignlib_lite.py_Protein20)) alignlib_lite.py_setDefaultLogOddor( alignlib_lite.py_makeLogOddorDirichlet(0.3)) alignlib_lite.py_setDefaultRegularizor( alignlib_lite.py_makeRegularizorDirichletPrecomputed()) cprofile1 = alignlib_lite.py_makeProfile(cmali1) cprofile2 = alignlib_lite.py_makeProfile(cmali2) result = alignlib_lite.py_makeAlignmentVector() alignator.align(result, cprofile1, cprofile2) E.debug("result=\n%s" % alignlib_lite.py_AlignmentFormatEmissions(result)) cmali1.add(cmali2, result) outmali = Mali.convertAlignlib2Mali(cmali1, identifiers=mali1.getIdentifiers() + mali2.getIdentifiers()) outmali.writeToFile(options.stdout, format=options.format) # write footer and output benchmark information. E.Stop()
def main(argv=None): """script main. parses command line options in sys.argv, unless *argv* is given. """ if not argv: argv = sys.argv # setup command line parser parser = E.OptionParser( version= "%prog version: $Id: cgat_script_template.py 2871 2010-03-03 10:20:44Z andreas $", usage=globals()["__doc__"]) parser.add_option("-o", "--gop", dest="gop", type="float", help="gap opening penalty [default=%default].") parser.add_option("-e", "--gep", dest="gep", type="float", help="gap extension penalty [default=%default].") parser.add_option( "-m", "--mode", dest="mode", type="choice", choices=("global", "local"), help="alignment mode, global=nw, local=sw [default=%default].") parser.set_defaults( gop=-12.0, gep=-2.0, format="fasta", mode="local", ) # add common options (-h/--help, ...) and parse command line (options, args) = E.Start(parser, argv=argv) if len(args) != 2: raise ValueError( "please supply two multiple alignments in FASTA format.") mali1 = Mali.Mali() mali2 = Mali.Mali() E.info("read 2 multiple alignments") mali1.readFromFile(IOTools.openFile(args[0], "r"), format=options.format) mali2.readFromFile(IOTools.openFile(args[1], "r"), format=options.format) cmali1 = Mali.convertMali2Alignlib(mali1) cmali2 = Mali.convertMali2Alignlib(mali2) if options.mode == "local": mode = alignlib_lite.py_ALIGNMENT_LOCAL elif options.mode == "global": mode = alignlib_lite.py_ALIGNMENT_GLOBAL alignator = alignlib_lite.py_makeAlignatorDPFull(mode, options.gop, options.gep) alignlib_lite.py_setDefaultEncoder( alignlib_lite.py_getEncoder(alignlib_lite.py_Protein20)) alignlib_lite.py_setDefaultLogOddor( alignlib_lite.py_makeLogOddorDirichlet(0.3)) alignlib_lite.py_setDefaultRegularizor( alignlib_lite.py_makeRegularizorDirichletPrecomputed()) cprofile1 = alignlib_lite.py_makeProfile(cmali1) cprofile2 = alignlib_lite.py_makeProfile(cmali2) result = alignlib_lite.py_makeAlignmentVector() alignator.align(result, cprofile1, cprofile2) E.debug("result=\n%s" % alignlib_lite.py_AlignmentFormatEmissions(result)) cmali1.add(cmali2, result) outmali = Mali.convertAlignlib2Mali(cmali1, identifiers=mali1.getIdentifiers() + mali2.getIdentifiers()) outmali.writeToFile(options.stdout, format=options.format) # write footer and output benchmark information. E.Stop()