def getpeds():
''' Read the pedigrees from sample_pedigrees and return a dict '''
PEDDIR = os.path.abspath(os.path.join(os.path.abspath(__file__), '..', '..', 'sample_pedigrees'))
peds = {}
for filename in glob.glob(PEDDIR + '/*ped'):
ped = list(read_ped(filename).pedigrees)[0]
pedname = os.path.basename(filename)[:-4]
peds[pedname] = ped
return peds
def getpeds():
''' Read the pedigrees from sample_pedigrees and return a dict '''
PEDDIR = os.path.abspath(
os.path.join(os.path.abspath(__file__), '..', '..',
'sample_pedigrees'))
peds = {}
for filename in glob.glob(PEDDIR + '/*ped'):
ped = list(read_ped(filename).pedigrees)[0]
pedname = os.path.basename(filename)[:-4]
peds[pedname] = ped
return peds
shares = shares2
print 'Reading null distribution'
with open(ndf) as f:
nulldist = {}
for line in f:
l = line.strip().split()
fam = l[0]
values = np.array([float(x) for x in l[1:]])
nulldist[fam] = values
#with open(affectedf) as f:
# affecteds = { tuple(x.strip().split()) for x in f }
# fams = {x[0] for x in affecteds}
peds = read_ped(affectedf)
affecteds = {x for x in peds.individuals if x.phenotypes['affected']}
print '{} affected individuals'.format(len(affecteds))
for ind in peds.individuals:
if ind.phenotypes['affected'] and ind.is_marryin_founder():
ind.phenotypes['affected'] = None
#for a in affecteds.copy():
# if a.is_marryin_founder():
# print 'Removed affected marry-in founder %s' % a
# affecteds.remove(a)
affecteds = {x.full_label for x in peds.individuals if x.phenotypes['affected']}
print '{} affecteds after removing marry-in founders'.format(len(affecteds))
fams = {x[0] for x in affecteds}
parser.add_argument('--freq', dest='freqs', nargs=3, action='append')
parser.add_argument('--prefix', type=str, help='prefix for output file',
default='simulation')
parser.add_argument('--verbose', action='store_true', dest='verbosity',
help='Print verbose output')
parser.add_argument('--output-filter', dest='predicate', default=None,
choices=('affected','phenotyped'), action='store')
parser.add_argument('--compress', choices=('bzip2', 'gzip'), action='store')
parser.add_argument('--seed', type=int, help='Random seed', default=None)
args = parser.parse_args()
if args.seed is not None:
pydigree.set_seed(args.seed)
# Read the pedigrees
template = read_ped(args.template)
# Read the chromosomes
if not args.chromosomes:
print('No chromosomes specified!')
exit()
for cfile in args.chromosomes:
c = read_gs_chromosome_template(cfile)
template.add_chromosome(c)
for freq in args.freqs:
chr, idx, maf = freq
maf = float(maf)
chr, idx = int(chr), int(idx)
# TODO: Sort out frequency semantics
template.chromosomes[chr].frequencies[idx] = 1-maf
parser.add_argument('--freq', dest='freqs', nargs=3, action='append')
parser.add_argument('--prefix', type=str, help='prefix for output file',
default='simulation')
parser.add_argument('--verbose', action='store_true', dest='verbosity',
help='Print verbose output')
parser.add_argument('--output-filter', dest='predicate', default=None,
choices=('affected', 'phenotyped'), action='store')
parser.add_argument('--compress', choices=('bzip2', 'gzip'), action='store')
parser.add_argument('--seed', type=int, help='Random seed', default=None)
args = parser.parse_args()
if args.seed is not None:
pydigree.set_seed(args.seed)
# Read the pedigrees
template = read_ped(args.template)
# Read the chromosomes
if not args.chromosomes:
print('No chromosomes specified!')
exit()
for cfile in args.chromosomes:
c = read_gs_chromosome_template(cfile)
template.add_chromosome(c)
for freq in args.freqs:
chrom, idx, maf = freq
maf = float(maf)
chrom, idx = int(chrom), int(idx)
# TODO: Sort out frequency semantics
import os
import glob
from pydigree.io import read_ped
PEDDIR = os.path.abspath(os.path.join(os.path.abspath(__file__), '..', '..', 'sample_pedigrees'))
peds = {}
for filename in glob.glob(PEDDIR + '/*ped'):
ped = list(read_ped(filename).pedigrees)[0]
pedname = os.path.basename(filename)[:-4]
peds[pedname] = ped
def test_parents():
ped = peds['fullsib']
ped['1'].parents() == (None, None)
ped['3'].parents() == (ped['1'], ped['2'])
def test_isfounder():
ped = peds['first_cousins']
assert ped['1'].is_founder()
assert not ped['3'].is_founder()
assert ped['4'].is_founder()
def test_depth():
ped = peds['first_cousins']
# Parental generation
assert ped['1'].depth == 0
# Marryin founder
assert ped['4'].depth == 0
# F1