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)
