def gen_x_chr(reference_file: str, working_folder: str, idx_run: int,
idx_perm: int, idx_m: int, idx_f: int, n_male: int,
n_female: int, xchr_male: [str], xchr_female: [str],
gender_perm: [[int]]):
pedigree = DefaultPedigree()
id_no_gender = ["Offspring3", "Offspring8", "Offspring17"]
parents_ids = pedigree.get_parents_ids()
# get the gender for the pedigree and randomize gender for the unknowns
gender = pedigree.get_pedigree_gender()
ids = pedigree.get_pedigree_ids()
ped_male = 0
ped_female = 0
for idx_g in range(len(gender)):
if gender[idx_g] == -1:
if ids[idx_g] == id_no_gender[0]:
gender[idx_g] = gender_perm[idx_perm][0]
elif ids[idx_g] == id_no_gender[1]:
gender[idx_g] = gender_perm[idx_perm][1]
elif ids[idx_g] == id_no_gender[2]:
gender[idx_g] = gender_perm[idx_perm][2]
else:
print("Unknown ID: {}".format(ids[idx_g]))
gender[idx_g] = random.choice([0, 1])
if gender[idx_g] == 0:
ped_female = ped_female + 1
elif gender[idx_g] == 1:
ped_male = ped_male + 1
pedigree_str = "pedigree_{}".format(idx_run + 1)
pedigree_folder = pedigree_str
if working_folder is not None:
pedigree_folder = os.path.join(working_folder, pedigree_folder)
# create folder for the current run
os.makedirs(pedigree_folder)
if idx_m + ped_male >= n_male:
random.shuffle(xchr_male)
idx_m = 0
if idx_f + ped_female >= n_female:
random.shuffle(xchr_female)
idx_f = 0
# now we have the female and male candidates
pedigree = []
for idx_ind, id_ind in enumerate(ids):
ind = Individual(ind_id=id_ind)
ind.set_gender(gender=gender[idx_ind])
if "Founder" in ind.id:
if gender[idx_ind] == 0:
x = xchr_female[idx_f]
idx_f = idx_f + 1
else:
x = xchr_male[idx_m]
idx_m = idx_m + 1
ind.set_x_chromosome(x_chromosome=x)
else:
ind.set_parents([
lib.get_individual(pedigree, parents_ids[idx_ind][0]),
lib.get_individual(pedigree, parents_ids[idx_ind][1])
])
ind.x_breed()
pedigree.append(ind)
# save the population
x_pedigree_file = "{}/x_{}.vcf".format(pedigree_folder, pedigree_str)
lib.export2vcf(population=pedigree,
vcf_header_template=reference_file,
vcf_file=x_pedigree_file,
save_all=True,
x_chromosome=True)
def init_autosome_pedigrees(founders_file: str,
n_pedigree=1,
output_folder=None,
feedback=True):
"""
Generate multiple autosome pedigrees (n_pedigree) starting from a reference VCF file (founders_file) that contains
candidate founders from which the pedigrees are developed.
:param str founders_file : The autosome reference VCF file that contains candidate founders for the pedigrees.
:param int, optional n_pedigree : The number of pedigrees that should be created. Optional parameter with default
value equal to 1.
:param str, optional output_folder : An output folder that should be created where all the pedigrees are stored.
Optional parameter, when not defined the folders of each pedigree are created in the current working directory.
N.B. The output folder should not exists. It will be created during the process. If the folder already exists,
the script will terminate with an error.
:param bool, optional feedback : If the flag is set to True it will provide a visual feedback of the ongoing
process, otherwise it will run silently with only minimal output.
"""
# create output folder if necessary
if output_folder is not None:
if feedback:
msg = "Initializing output folder '{}'".format(output_folder)
sys.stdout.write(msg)
sys.stdout.flush()
os.makedirs(output_folder) # create output folder
if feedback:
sys.stdout.write(" [OK]")
sys.stdout.flush()
name, file_extension = os.path.splitext(
founders_file) # separate filename and extension
if feedback:
msg = "\nLoad candidate founders"
sys.stdout.write(msg)
sys.stdout.flush()
unrelated_id = lib.individuals_in_vcf(
founders_file) # IDs of unrelated individuals
random.shuffle(
unrelated_id
) # random shuffling of the unrelated individuals to be selected as founders
# check of having a sufficient number of unrelated individuals (i.e., 8) for the standard pedigree
if len(unrelated_id) < 8:
raise ValueError(
"The population of unrelated individuals should have at least 8 members."
)
if feedback:
sys.stdout.write(" [OK]\n")
sys.stdout.flush()
pedigree = DefaultPedigree()
offset = 0 # used to select different founders for each run (reshuffle when all unrelated individuals are used)
for idx_run in range(n_pedigree):
if feedback:
msg = "\nInitialization of pedigree {} ".format(idx_run + 1)
with Spinner(msg):
# create folder for the current run
run_folder = "pedigree_{}".format(idx_run + 1)
if output_folder is not None:
run_folder = os.path.join(output_folder, run_folder)
os.makedirs(run_folder)
# random selection of founders
if 8 * offset + 8 >= len(
unrelated_id
): # reached end of the list, cannot find additional 8 founders
offset = 0 # restart the selection
random.shuffle(
unrelated_id
) # new shuffling of unrelated individuals to be selected as founders
founder = unrelated_id[8 * offset:8 * offset + 8]
# create the population based on the defined pedigree for the current run
run_pop = pedigree.get_pedigree(founders_file, founder)
sys.stdout.write("[OK]")
sys.stdout.flush()
msg = "\nSave pedigree {} in folder '{}'".format(
idx_run + 1, run_folder)
sys.stdout.write(msg)
else:
# create folder for the current run
run_folder = "pedigree_{}".format(idx_run + 1)
if output_folder is not None:
run_folder = os.path.join(output_folder, run_folder)
os.makedirs(run_folder)
# random selection of founders
if 8 * offset + 8 >= len(
unrelated_id
): # the end of the list was reached, cannot find addition 8 founders
offset = 0 # restart the selection
random.shuffle(
unrelated_id
) # new random shuffling of unrelated individuals to be selected as founders
founder = unrelated_id[8 * offset:8 * offset + 8]
# create the population based on the defined pedigree for the current run
run_pop = pedigree.get_pedigree(founders_file, founder)
# save the population
pedigree_file = "pedigree_{}{}".format(idx_run + 1, file_extension)
population_file = "pedigree_{}{}".format(idx_run + 1, ".pop")
lib.export2vcf(population=run_pop,
vcf_header_template=founders_file,
vcf_file=os.path.join(run_folder, pedigree_file))
lib.save_object(run_pop, os.path.join(run_folder, population_file))
if feedback:
sys.stdout.write(" [OK]\n")
sys.stdout.flush()
offset = offset + 1
if feedback:
sys.stdout.write("\n")
sys.stdout.flush()