def __init__(self, extra): """Initializes the IQTREE model""" StatModel.__init__(self, extra) self.VERSION = "1.0" parser = optparse.OptionParser(prog="IQTREEModel") parser.add_option("-c", "--cpu", dest="cpu", metavar="<cpu>", default=1, help="number of threads to use (default: 1)") parser.add_option("-m", "--model", dest="model", metavar="<model>", default="GTR+G", help="model of DNA, AA, or CODON substitution (default: GTR+G)") parser.add_option("-t", "--type", dest="type", metavar="<type>", default="DNA", help="data type, one of the following: DNA, AA, NT2AA, CODON (default: DNA)") parser.add_option("-z", "--test", dest="test", metavar="", default="SH", help="tree topology test, one of the following: SH, AU (default: SH)") parser.add_option("-r", "--replicates", dest="rep", metavar="<rep>", default=1, help="number of RELL replicates for the tree topology test (default: 1)") parser.add_option("-p", "--prefix", dest="pre", metavar="<pre>", default="", help="the prefix for temporary output files (default: '')") self.parser = parser StatModel._parse_args(self, extra)
def optimize_model(self, gtree, aln): """Optimizes the RAxML model""" StatModel.optimize_model(self, gtree, aln) fd, treefile = tempfile.mkstemp('.tree') os.close(fd) gtree.write(treefile) fd, seqfile = tempfile.mkstemp('.align') os.close(fd) out = util.open_stream(seqfile, "w") phylip.write_phylip_align(out, aln, strip_names=False) out.close() self._raxml.optimize_model(treefile, seqfile, "-m %s -e %s -n test" % (self.model, self.eps)) os.remove(treefile) os.remove(seqfile)
def __init__(self, extra): """Initializes the RAxML model""" StatModel.__init__(self, extra) self.VERSION = "0.2.4" self._raxml = raxml.RAxML() self.rooted = self._raxml.rooted parser = optparse.OptionParser(prog="RAxMLModel") parser.add_option("-m", "--model", dest="model", metavar="<model>", default="GTRGAMMA", help="model of nucleotide or amino acid substitution (default: GTRGAMMA)") parser.add_option("-e", "--eps", dest="eps", metavar="<eps>", default=2.0, type="float", help="model optimization precision in log likelihood units (default 2.0)") self.parser = parser StatModel._parse_args(self, extra)