def __init__(self, extra):
"""Initializes the model"""
CostModel.__init__(self, extra)
self.VERSION = "1.0.1"
self.mincost = 0
parser = optparse.OptionParser(prog="DupLossModel")
parser.add_option(
"-D",
"--dupcost",
dest="dupcost",
metavar="<dup cost>",
default=1.0,
type="float",
help="duplication cost (default: 1.0)",
)
parser.add_option(
"-L",
"--losscost",
dest="losscost",
metavar="<loss cost>",
default=1.0,
type="float",
help="loss cost (default: 1.0)",
)
self.parser = parser
CostModel._parse_args(self, extra)
def __init__(self, extra):
"""Initializes the model"""
CostModel.__init__(self, extra)
self.VERSION = "0.1.0"
self.mincost = 0
parser = optparse.OptionParser(prog="DTLModel")
parser.add_option("-D", "--dupcost", dest="dupcost",
metavar="<dup cost>",
default=2, type="int",
help="duplication cost (default: 2)")
parser.add_option("-T", "--transfercost", dest="transfercost",
metavar="<transfer cost>",
default=3, type="int",
help="transfer cost (default: 3)")
parser.add_option("-L", "--losscost", dest="losscost",
metavar="<loss cost>",
default=1, type="int",
help="loss cost (default: 1)")
self.parser = parser
CostModel._parse_args(self, extra)
# make temporary file
fd, self.treefile = tempfile.mkstemp()
os.close(fd)
def __init__(self, extra):
"""Initializes the model"""
CostModel.__init__(self, extra)
self.VERSION = "0.1.0"
self.mincost = 0
CostModel._parse_args(self, extra)
# make temporary file
fd, self.treefile = tempfile.mkstemp()
os.close(fd)
def __init__(self, extra):
"""Initializes the model"""
CostModel.__init__(self, extra)
self.VERSION = "0.1.2"
self.mincost = 0
parser = optparse.OptionParser(prog="DTLModel")
parser.add_option("--cmd", dest="cmd",
metavar="<ranger-dtl-U command>",
default="ranger-dtl-U",
help="ranger-dtl-U command (default: \"ranger-dtl-U\")")
parser.add_option("-D", "--dupcost", dest="dupcost",
metavar="<duplication cost>",
default=2, type="int",
help="duplication cost, integer only (default: 2)")
parser.add_option("-T", "--transcost", "--transfercost", dest="transcost",
metavar="<transfer cost>",
default=3, type="int",
help="transfer cost, integer only (default: 3)")
parser.add_option("-L", "--losscost", dest="losscost",
metavar="<loss cost>",
default=1, type="int",
help="loss cost, integer only (default: 1)")
parser.add_option("--seed", dest="seed",
metavar="<seed>",
type="int",
help="user defined random number generator seed")
parser.add_option("--tmp", dest="tmp",
metavar="<tmp directory>",
help="directory for temporary files (must exist)")
self.parser = parser
CostModel._parse_args(self, extra)
# check temporary directory
if self.tmp:
if not os.path.exists(os.path.realpath(self.tmp)):
raise Exception("--tmp directory does not exist")
# make temporary file
fd, self.treefile = tempfile.mkstemp(dir=self.tmp)
os.close(fd)
# hack for cygwin (ranger-dtl-U cannot handle system files)
if sys.platform == 'cygwin':
cwd = os.getcwd()
if self.treefile.startswith(cwd):
# remove working path (and backslash)
self.treefile = self.treefile[len(cwd)+1:]
else:
raise Exception("--tmp must be a relative path when using cygwin")
def __init__(self, extra):
"""Initializes the model"""
CostModel.__init__(self, extra)
self.VERSION = "0.1.0"
self.mincost = -util.INF
parser = optparse.OptionParser(prog="SpimapModel")
parser.add_option("-a", "--align", dest="align",
metavar="<alignment fasta>",
help="sequence alignment in fasta format")
parser.add_option("-p", "--param", dest="params",
metavar="<params file>",
help="substitution rate parameters file")
parser.add_option("--simplereroot", dest="simplereroot",
metavar="<simple reroot>",
default=False, action="store_true",
help="set to reroot using dup/loss cost")
grp_seq = optparse.OptionGroup(parser, "Sequence evolution model")
grp_seq.add_option("-k", "--kappa", dest="kappa",
metavar="<transition/transversion estimate>",
default=-1.0, type="float",
help="used for HKY model (default: estimate)")
grp_seq.add_option("-f", "--bgfreq", dest="bgfreq",
metavar="<A freq>,<C freq>,<G freq>,<T freq>",
help="background frequencies (default: estimate)")
parser.add_option_group(grp_seq)
grp_duploss = optparse.OptionGroup(parser, "Dup/loss evolution model")
grp_duploss.add_option("-D", "--duprate", dest="duprate",
metavar="<duplication rate>",
default=0.1, type="float",
help="rate of gene duplication (default: 0.1)")
grp_duploss.add_option("-L", "--lossrate", dest="lossrate",
metavar="<loss rate>",
default=0.1, type="float",
help="rate of gene loss (default: 0.1)")
grp_duploss.add_option("-P", "--pretime", dest="pretime",
metavar="<pre-speciation time parameter>",
default=1.0, type="float",
help="lambda param of pre-speciation distribution (default: 1.0)")
parser.add_option_group(grp_duploss)
self.parser = parser
CostModel._parse_args(self, extra)
def __init__(self, extra):
"""Initializes the model"""
CostModel.__init__(self, extra)
self.VERSION = "0.1.0"
self.mincost = 0
parser = optparse.OptionParser(prog="DLCModel")
parser.add_option("-D", "--dupcost", dest="dupcost",
metavar="<dup cost>",
default=1.0, type="float",
help="duplication cost (default: 1.0)")
parser.add_option("-L", "--losscost", dest="losscost",
metavar="<loss cost>",
default=1.0, type="float",
help="loss cost (default: 1.0)")
parser.add_option("-C", "--coalcost", dest="coalcost",
metavar="<(deep) coalescence cost>",
default=1.0, type="float",
help="deep coalescence cost (default: 1.0)")
parser.add_option("-o", "--output", dest="output",
metavar="<locus tree output file>",
help="locus tree output file")
grp_search = optparse.OptionGroup(parser, "Search Options")
grp_search.add_option("--dcs", dest="dcs",
metavar="<DCS threshold>",
default=0.25, type="float",
help="duplication consistency score threshold: " +
"DCS >/<= thr resolves to DUP/ILS (default: 0)")
grp_search.add_option("--switch", dest="switch",
default=False, action="store_true",
help="switches equality assignment for DCS threshold, " +
"i.e. DCS >=/< thr resolves to DUP/ILS")
parser.add_option_group(grp_search)
self.parser = parser
CostModel._parse_args(self, extra)
self.locustree = None
