def main(options):
"""
read and convert.
"""
if options["msmc"] and len(options["individuals"]) not in [2,4]:
raise Exception("msmc output needs either 2 or 4 individuals")
if options["psmc"] and len(options["individuals"]) not in [1,2]:
raise Exception("psmc output needs either 1 or 2 individuals")
index=read_sample(options["shapeit"]+".sample", options["individuals"])
index=index_to_index(index)
try:
hap_file=gzip.open(options["shapeit"]+".haps.gz", "r")
except IOError:
hap_file=open(options["shapeit"]+".haps", "r")
chr=np.genfromtxt(hap_file, dtype=str, usecols=0)
hap_file.seek(0)
pos=np.genfromtxt(hap_file, dtype=int, usecols=2)
hap_file.seek(0)
alleles=np.genfromtxt(hap_file, dtype=str, usecols=(3,4))
hap_file.seek(0)
haps=np.genfromtxt(hap_file, dtype=int, usecols=5+index)
if options["msmc"]:
gdc.output_msmc(haps, chr, pos, alleles, options)
if options["psmc"]:
gdc.output_psmc(haps, chr[0], pos, options) #Assumes all on the same chromosome
def main(options):
"""
read and convert.
"""
length,pos,haps=read_macs(options["macs"])
npos,nhaps=haps.shape
if nhaps not in [2,4,8]:
raise Exception("Must have 2,4 or 8 haplotypes")
if options["switch_rate"]>0 or options["flip_rate"]>0:
site_switch_rate=options["switch_rate"]*length/len(pos)
site_flip_rate=options["flip_rate"]*length/len(pos)
for i in range(int(nhaps/2)):
haps[:,[2*i,2*i+1]]=add_phasing_errors(haps[:,[2*i,2*i+1]], site_switch_rate, site_flip_rate)
alleles=np.zeros( (npos,2), dtype=str)
alleles[:,0]="A"
alleles[:,1]="T"
if options["msmc"]:
chrs=np.zeros(npos, dtype=str,)
chrs[:]=options["chr"]
gdc.output_msmc(haps, chrs, pos, alleles, options)
if options["psmc"]:
gdc.output_psmc(haps, options["chr"], pos, options) #Assumes all on the same chromosome
def main(options):
"""
read and convert.
"""
length, pos, haps = read_ms(options["ms"], options)
npos, nhaps = haps.shape
if nhaps not in [2, 4, 8]:
raise Exception("Must have 2,4 or 8 haplotypes")
if options["switch_rate"] > 0 or options["flip_rate"] > 0:
site_switch_rate = options["switch_rate"] * length / len(pos)
site_flip_rate = options["flip_rate"] * length / len(pos)
for i in range(int(nhaps / 2)):
haps[:, [2 * i, 2 * i + 1]] = add_phasing_errors(
haps[:, [2 * i, 2 * i + 1]], site_switch_rate, site_flip_rate)
alleles = np.zeros((npos, 2), dtype=str)
alleles[:, 0] = "A"
alleles[:, 1] = "T"
if options["msmc"]:
chrs = np.zeros(
npos,
dtype=str,
)
chrs[:] = options["chr"]
gdc.output_msmc(haps, chrs, pos, alleles, options)
if options["psmc"]:
gdc.output_psmc(haps, options["chr"], pos,
options) #Assumes all on the same chromosome
def main(options):
"""
read and convert.
"""
if options["msmc"] and len(options["individuals"]) not in [2, 4]:
raise Exception("msmc output needs either 2 or 4 individuals")
if options["psmc"] and len(options["individuals"]) not in [1, 2]:
raise Exception("psmc output needs either 1 or 2 individuals")
index = read_sample(options["shapeit"] + ".sample", options["individuals"])
index = index_to_index(index)
try:
hap_file = gzip.open(options["shapeit"] + ".haps.gz", "r")
except IOError:
hap_file = open(options["shapeit"] + ".haps", "r")
chr = np.genfromtxt(hap_file, dtype=str, usecols=0)
hap_file.seek(0)
pos = np.genfromtxt(hap_file, dtype=int, usecols=2)
hap_file.seek(0)
alleles = np.genfromtxt(hap_file, dtype=str, usecols=(3, 4))
hap_file.seek(0)
haps = np.genfromtxt(hap_file, dtype=int, usecols=5 + index)
if options["msmc"]:
gdc.output_msmc(haps, chr, pos, alleles, options)
if options["psmc"]:
gdc.output_psmc(haps, chr[0], pos,
options) #Assumes all on the same chromosome