def __init__(self, options):
super(_IsolationInitialMigration3HMMModel, self).__init__()
alignments_src1_admix = _prepare_alignments(options, 'ziphmm_src1_admix')
alignments_src1_scr1 = _prepare_alignments(options, 'ziphmm_scr1_scr1')
alignments_admix_admix = _prepare_alignments(options, 'ziphmm_admix_admix')
self.forwarders_src1_admix = [Forwarder.fromDirectory(arg) for arg in alignments_src1_admix]
self.forwarders_src1_src1 = [Forwarder.fromDirectory(arg) for arg in alignments_src1_scr1]
self.forwarders_admix_admix = [Forwarder.fromDirectory(arg) for arg in alignments_admix_admix]
def __init__(self, options):
super(_ThreePopAdmix23Model, self).__init__()
alignments_src1_admix = _prepare_alignments(options, 'ziphmm_src1_admix')
alignments_src2_admix = _prepare_alignments(options, 'ziphmm_src2_admix')
alignments_src1_src2 = _prepare_alignments(options, 'ziphmm_src1_src2')
self.forwarders_src1_admix = [Forwarder.fromDirectory(arg) for arg in alignments_src1_admix]
self.forwarders_src2_admix = [Forwarder.fromDirectory(arg) for arg in alignments_src2_admix]
self.forwarders_src1_src2 = [Forwarder.fromDirectory(arg) for arg in alignments_src1_src2]
def __init__(self, options):
super(_ThreePopAdmix23Model15HMM, self).__init__()
alignments_src1_admix = [_prepare_alignments(options, 'ziphmm_src1_admix'),
_prepare_alignments(options, 'ziphmm_src1_admix_2'),
_prepare_alignments(options, 'ziphmm_src1_admix_3'),
_prepare_alignments(options, 'ziphmm_src1_admix_4')]
alignments_src2_admix = [_prepare_alignments(options, 'ziphmm_src2_admix'),
_prepare_alignments(options, 'ziphmm_src2_admix_2'),
_prepare_alignments(options, 'ziphmm_src2_admix_3'),
_prepare_alignments(options, 'ziphmm_src2_admix_4')]
alignments_src1_src2 = [_prepare_alignments(options, 'ziphmm_src1_src2'),
_prepare_alignments(options, 'ziphmm_src1_src2_2'),
_prepare_alignments(options, 'ziphmm_src1_src2_3'),
_prepare_alignments(options, 'ziphmm_src1_src2_4')]
alignments_src1_scr1 = _prepare_alignments(options, 'ziphmm_scr1_scr1')
alignments_src2_src2 = _prepare_alignments(options, 'ziphmm_src2_src2')
alignments_admix_admix = _prepare_alignments(options, 'ziphmm_admix_admix')
self.forwarders_src1_admix = [[Forwarder.fromDirectory(arg) for arg in algs] for algs in alignments_src1_admix]
self.forwarders_src2_admix = [[Forwarder.fromDirectory(arg) for arg in algs] for algs in alignments_src2_admix]
self.forwarders_src1_src2 = [[Forwarder.fromDirectory(arg) for arg in algs] for algs in alignments_src1_src2]
self.forwarders_src1_src1 = [Forwarder.fromDirectory(arg) for arg in alignments_src1_scr1]
self.forwarders_src2_src2 = [Forwarder.fromDirectory(arg) for arg in alignments_src2_src2]
self.forwarders_admix_admix = [Forwarder.fromDirectory(arg) for arg in alignments_admix_admix]
def main():
usage = """%prog [options] <input> <input format> <output dir>
This program reads in an input sequence in any format supported by BioPython
and writes out a preprocessed file ready for use with zipHMM.
Also supports gzipped input files, if the name ends with `.gz`.
Assumption #1: Either the file is a pairwise alignment, or you have provided
exactly two names to the `--names` option.
Assumption #2: The file uses a simple ACGT format (and N/-). Anything else will
be interpreted as N and a warning will be given with all unknown symbols.
Warning: This program uses SeqIO.to_dict to read in the entire alignment, you
may want to split the alignment first if it's very large.
"""
parser = OptionParser(usage=usage, version="%prog 1.0")
parser.add_option(
"--names",
dest="names",
type="string",
default=None,
help="A comma-separated list of names to use from the source file",
)
parser.add_option("-v", "--verbose", dest="verbose", action="store_true", default=False, help="Print some stuff")
(options, args) = parser.parse_args()
if len(args) != 3:
parser.error("Needs input file, input format and output file")
in_filename = args.pop(0)
in_format = args.pop(0)
output_dirname = args.pop(0)
assert os.path.exists(in_filename), "Must use an existing input file"
if in_filename.endswith(".gz"):
if options.verbose:
print "Assuming '%s' is a gzipped file." % in_filename
inf = gzip.open(in_filename)
else:
inf = open(in_filename)
if options.verbose:
print "Loading data...",
sys.stdout.flush()
alignments = SeqIO.to_dict(SeqIO.parse(inf, in_format))
if options.verbose:
print "done"
if options.names:
names = options.names.split(",")
else:
names = list(alignments.keys())
assert len(names) == 2, "Must be a pairwise alignment."
if options.verbose:
print "Assuming pairwise alignment between '%s' and '%s'" % (names[0], names[1])
srcs = [alignments[name].seq for name in names]
clean = set("ACGT")
A = srcs[0]
B = srcs[1]
assert len(A) == len(B)
L = len(A)
fd, foutname = tempfile.mkstemp()
if options.verbose:
print "Writing temp file readable by zipHMM to '%s'..." % (foutname),
sys.stdout.flush()
seen = set()
with os.fdopen(fd, "w", 64 * 1024) as f:
for i in xrange(L):
s1, s2 = A[i].upper(), B[i].upper()
seen.add(s1)
seen.add(s2)
if s1 not in clean or s2 not in clean:
print >> f, 2,
elif s1 == s2:
print >> f, 0,
else:
print >> f, 1,
if options.verbose:
print "done"
if len(seen - set("ACGTN-")) > 1:
print >> sys.stderr, "I didn't understand the following symbols form the input sequence: %s" % (
"".join(list(seen - set("ACGTN-")))
)
if options.verbose:
print "zipHMM is preprocessing...",
sys.stdout.flush()
f = Forwarder.fromSequence(seqFilename=foutname, alphabetSize=3, minNoEvals=500)
if options.verbose:
print "done"
if options.verbose:
print "Writing zipHMM data to '%s'..." % (output_dirname),
sys.stdout.flush()
if not os.path.exists(output_dirname):
os.makedirs(output_dirname)
f.writeToDirectory(output_dirname)
os.rename(foutname, os.path.join(output_dirname, "original_sequence"))
if options.verbose:
print "done"
def main():
"""
Run the main script.
"""
usage = """%(prog)s [options] <forwarder dirs>
This program estimates the parameters of an isolation model with two species
and uniform coalescence and recombination rates."""
parser = ArgumentParser(usage=usage, version="%(prog)s 1.1")
parser.add_argument("--header",
action="store_true",
default=False,
help="Include a header on the output")
parser.add_argument("-o",
"--outfile",
type=str,
default="/dev/stdout",
help="Output file for the estimate (/dev/stdout)")
parser.add_argument(
"--logfile",
type=str,
default=None,
help="Log for all points estimated in the optimization")
parser.add_argument(
"--states-12",
type=int,
default=10,
help=
"Number of intervals used to discretize the time between the first and second speciation (10)"
)
parser.add_argument(
"--states-123",
type=int,
default=10,
help=
"Number of intervals used to discretize the time after the second speciation (10)"
)
parser.add_argument(
"--optimizer",
type=str,
default="Nelder-Mead",
help=
"Optimization algorithm to use for maximizing the likelihood (Nealder-Mead)",
choices=['Nelder-Mead', 'Powell', 'L-BFGS-B', 'TNC'])
parser.add_argument(
"--outgroup",
action="store_true",
default=None,
help="Outgroup is included as fourth sequence in alignment.")
optimized_params = [
('split-12', 'First split time in substitutions', 1e6 / 1e9),
('split-123', 'Second split time in substitutions', 1e6 / 1e9),
('theta-1',
'effective population size in 4Ne substitutions for species 1',
1e6 / 1e9),
('theta-2',
'effective population size in 4Ne substitutions for species 2',
1e6 / 1e9),
('theta-3',
'effective population size in 4Ne substitutions for species 3',
1e6 / 1e9),
('theta-12',
'effective population size in 4Ne substitutions for species 12 (first ancestral)',
1e6 / 1e9),
('theta-123',
'effective population size in 4Ne substitutions for species 123 (ancestral to all)',
1e6 / 1e9), ('rho', 'recombination rate in substitutions', 0.4),
('outgroup', 'total height of tree with outgroup', 1e6 / 1e9)
]
for parameter_name, description, default in optimized_params:
parser.add_argument("--%s" % parameter_name,
type=float,
default=default,
help="Initial guess at the %s (%g)" %
(description, default))
parser.add_argument('alignments',
nargs='+',
help='Alignments in ZipHMM format')
options = parser.parse_args()
if len(options.alignments) < 1:
parser.error("Input alignment not provided!")
init_parameters = (options.split_12, options.split_123,
1 / (options.theta_1 / 2), 1 / (options.theta_2 / 2),
1 / (options.theta_3 / 2), 1 / (options.theta_12 / 2),
1 / (options.theta_123 / 2), options.rho)
if options.outgroup:
init_parameters += (options.outgroup, )
output_header = [
'split.time.12', 'split.time.123', 'theta.1', 'theta.2', 'theta.3',
'theta.12', 'theta.123', 'rho'
]
if options.outgroup:
output_header.append("outgroup")
forwarders = [Forwarder.fromDirectory(arg) for arg in options.alignments]
log_likelihood = Likelihood(
ILSModel(options.states_12, options.states_123), forwarders)
if options.logfile:
with open(options.logfile, 'w') as logfile:
if options.header:
print >> logfile, '\t'.join(output_header)
mle_parameters = maximum_likelihood_estimate(
log_likelihood,
init_parameters,
optimizer_method=options.optimizer,
log_file=logfile,
log_param_transform=transform)
else:
mle_parameters = maximum_likelihood_estimate(
log_likelihood,
init_parameters,
optimizer_method=options.optimizer)
max_log_likelihood = log_likelihood(mle_parameters)
with open(options.outfile, 'w') as outfile:
if options.header:
print >> outfile, '\t'.join(output_header)
print >> outfile, '\t'.join(
map(str,
transform(mle_parameters) + (max_log_likelihood, )))
def main():
usage = """%prog [options] <forwarder dirs>
This program estimates the parameters of an isolation model with two species
and uniform coalescence/recombination rate."""
parser = OptionParser(usage=usage, version="%prog 1.0")
parser.add_option("-o",
"--out",
dest="outfile",
type="string",
default="/dev/stdout",
help="Output file for the estimate (/dev/stdout)")
parser.add_option(
"--tmpfile",
dest="tmpfile",
type="string",
default="/dev/null",
help="Log for all points estimated in the optimization (/dev/null)")
optimized_params = [
('splittime', 'split time', 1e6),
('Ne', 'effective population size', 20e3),
('recomb', 'recombination rate', 0.1),
]
for (cname, desc, default) in optimized_params:
parser.add_option("--%s" % cname,
dest=cname,
type="float",
default=default,
help="Initial guess at the %s (%g)" %
(desc, default))
fixed_params = [
('mu', 'mutation rate', 1e-9),
('g', 'generation time', 20),
]
for (cname, desc, default) in fixed_params:
parser.add_option("--%s" % cname,
dest=cname,
type="float",
default=default,
help="Value of the %s (%g)" % (desc, default))
parser.add_option(
"--intervals",
dest="intervals",
type="int",
default=10,
help="Number of sub intervals used to discretize the time (10)")
parser.add_option("--header",
dest="include_header",
action="store_true",
default=False,
help="Include a header on the output")
parser.add_option("-v",
"--verbose",
dest="verbose",
action="store_true",
default=False,
help="Print help")
(options, args) = parser.parse_args()
if len(args) < 1:
parser.error("Needs at least one preprocessed sequence to work on")
if not options.verbose:
log = lambda s: None
logu = lambda s: None
else:
logu = log_unfinished_line
log = log_finished_line
logu("Loading forwarders...")
forwarders = [Forwarder.fromDirectory(dir) for dir in args]
log("done")
logu("Constructing model...")
intervals = options.intervals
modelI = build_epoch_seperated_model(2, [[0, 0]], [1, intervals])
log("done")
mu = options.mu
g = options.g
T = options.splittime * mu
C = 1.0 / (g * mu * 2 * options.Ne)
R = options.recomb
with open(options.tmpfile, 'w') as tmpfile:
L, est = estimate_I(modelI, forwarders, T, C, R, outfile=tmpfile)
vals = "\t".join(map(str, est))
with open(options.outfile, 'w') as outfile:
if options.include_header:
print >> outfile, 'logL\tT\tC\tR'
print >> outfile, "%f\t%s" % (L, vals)
def main():
usage = """%prog [options] <input> <input format> <output dir>
This program reads in an input sequence in any format supported by BioPython
and writes out a preprocessed file ready for use with zipHMM.
Also supports gzipped input files, if the name ends with `.gz`.
Assumption #1: Either the file is a pairwise alignment, or you have provided
exactly two names to the `--names` option.
Assumption #2: The file uses a simple ACGT format (and N/-). Anything else will
be interpreted as N and a warning will be given with all unknown symbols.
Warning: This program uses SeqIO.to_dict to read in the entire alignment, you
may want to split the alignment first if it's very large.
"""
parser = OptionParser(usage=usage, version="%prog 1.0")
parser.add_option(
"--names",
dest="names",
type="string",
default=None,
help="A comma-separated list of names to use from the source file")
parser.add_option("-v",
"--verbose",
dest="verbose",
action="store_true",
default=False,
help="Print some stuff")
(options, args) = parser.parse_args()
if len(args) != 3:
parser.error("Needs input file, input format and output file")
in_filename = args.pop(0)
in_format = args.pop(0)
output_dirname = args.pop(0)
assert os.path.exists(in_filename), "Must use an existing input file"
if in_filename.endswith('.gz'):
if options.verbose:
print "Assuming '%s' is a gzipped file." % in_filename
inf = gzip.open(in_filename)
else:
inf = open(in_filename)
if options.verbose:
print "Loading data...",
sys.stdout.flush()
alignments = SeqIO.to_dict(SeqIO.parse(inf, in_format))
if options.verbose:
print "done"
if options.names:
names = options.names.split(',')
else:
names = list(alignments.keys())
assert len(names) == 2, "Must be a pairwise alignment."
if options.verbose:
print "Assuming pairwise alignment between '%s' and '%s'" % (names[0],
names[1])
srcs = [alignments[name].seq for name in names]
clean = set('ACGT')
A = srcs[0]
B = srcs[1]
assert len(A) == len(B)
L = len(A)
fd, foutname = tempfile.mkstemp()
if options.verbose:
print "Writing temp file readable by zipHMM to '%s'..." % (foutname),
sys.stdout.flush()
seen = set()
with os.fdopen(fd, 'w', 64 * 1024) as f:
for i in xrange(L):
s1, s2 = A[i].upper(), B[i].upper()
seen.add(s1)
seen.add(s2)
if s1 not in clean or s2 not in clean:
print >> f, 2,
elif s1 == s2:
print >> f, 0,
else:
print >> f, 1,
if options.verbose:
print "done"
if len(seen - set('ACGTN-')) > 1:
print >> sys.stderr, "I didn't understand the following symbols form the input sequence: %s" % (
''.join(list(seen - set('ACGTN-'))))
if options.verbose:
print "zipHMM is preprocessing...",
sys.stdout.flush()
f = Forwarder.fromSequence(seqFilename=foutname,
alphabetSize=3,
minNoEvals=500)
if options.verbose:
print "done"
if options.verbose:
print "Writing zipHMM data to '%s'..." % (output_dirname),
sys.stdout.flush()
if not os.path.exists(output_dirname):
os.makedirs(output_dirname)
f.writeToDirectory(output_dirname)
os.rename(foutname, os.path.join(output_dirname, 'original_sequence'))
if options.verbose:
print "done"
def __init__(self, options):
super(_IsolationModel, self).__init__()
alignments = _prepare_alignments(options, 'ziphmm_src1_admix')
self.forwarders = [Forwarder.fromDirectory(arg) for arg in alignments]
def __init__(self, options):
super(_TwoPopAdmix23OneSampleModel, self).__init__()
alignments_src1_admix = _prepare_alignments(options, 'ziphmm_src1_admix')
self.forwarders_src1_admix = [Forwarder.fromDirectory(arg) for arg in alignments_src1_admix]
def main():
usage="""%prog [options] <forwarder dirs>
This program estimates the parameters of an isolation model with two species
and uniform coalescence/recombination rate."""
parser = OptionParser(usage=usage, version="%prog 1.0")
parser.add_option("-o", "--out",
dest="outfile",
type="string",
default="/dev/stdout",
help="Output file for the estimate (/dev/stdout)")
parser.add_option("--tmpfile",
dest="tmpfile",
type="string",
default="/dev/null",
help="Log for all points estimated in the optimization (/dev/null)")
optimized_params = [
('splittime', 'split time', 1e6),
('Ne', 'effective population size', 20e3),
('recomb', 'recombination rate', 0.1),
]
for (cname, desc, default) in optimized_params:
parser.add_option("--%s" % cname,
dest=cname,
type="float",
default=default,
help="Initial guess at the %s (%g)" % (desc, default))
fixed_params = [
('mu', 'mutation rate', 1e-9),
('g', 'generation time', 20),
]
for (cname, desc, default) in fixed_params:
parser.add_option("--%s" % cname,
dest=cname,
type="float",
default=default,
help="Value of the %s (%g)" % (desc, default))
parser.add_option("--intervals",
dest="intervals",
type="int",
default=10,
help="Number of sub intervals used to discretize the time (10)")
parser.add_option("--header",
dest="include_header",
action="store_true",
default=False,
help="Include a header on the output")
parser.add_option("-v", "--verbose",
dest="verbose",
action="store_true",
default=False,
help="Print help")
(options, args) = parser.parse_args()
if len(args) < 1:
parser.error("Needs at least one preprocessed sequence to work on")
if not options.verbose:
log = lambda s: None
logu = lambda s: None
else:
logu = log_unfinished_line
log = log_finished_line
logu("Loading forwarders...")
forwarders = [Forwarder.fromDirectory(dir) for dir in args]
log("done")
logu("Constructing model...")
intervals = options.intervals
modelI = build_epoch_seperated_model(2, [[0,0]], [1,intervals])
log("done")
mu = options.mu
g = options.g
T = options.splittime * mu
C = 1.0/(g*mu*2*options.Ne)
R = options.recomb
with open(options.tmpfile, 'w') as tmpfile:
L, est = estimate_I(modelI, forwarders, T, C, R, outfile=tmpfile)
vals = "\t".join(map(str,est))
with open(options.outfile, 'w') as outfile:
if options.include_header:
print >>outfile, 'logL\tT\tC\tR'
print >>outfile, "%f\t%s" % (L,vals)