def xxxtest_check_consanguinity(self):
ped = Pedigree()
ped.load('../cplex/pedigree_50_4_8_2_G3.ped')
print(ped.all_consanguineous_ped(3))
print(ped.is_consanguineous('1','7',2))
print(ped.old_gen('1',4).intersection(ped.old_gen('7',4)))
print(ped.old_gen('7', 4))
print('---------------------------')
nb_ped = 50
nb_people = [10,20,50,100,200,300,500,1000,1500,2000,2200,2400]
nb_Gen_Max = [3,3,4,4,4,4,4,5,5,6,6,6]
# nb_people = [50]
# nb_Gen_Max = [4]
nb_Gen_Min = [math.ceil(x/2) for x in nb_Gen_Max]
cl = 3
cpt = 0
for p, g_max, g_min in zip(nb_people, nb_Gen_Max, nb_Gen_Min):
for nb in range(nb_ped):
nbChild = random.randint(4, 8)
g = random.randint(g_min, g_max)
ped = Pedigree()
ped.gen_ped(nb, p, g, nbChild, cl)
if len(ped.all_consanguineous_ped(cl)) != 0:
cpt+=1
print('ICI IL Y A UN PB',ped.all_consanguineous_ped(3))
print('le pedigree en question',ped)
pview.save(ped, f'../pedigree_{p}_{g}_{nbChild}_{cl - 1}_G{nb}')
pview.graph(ped, f'../generate_graph_{p}_{g}_{nbChild}_{cl - 1}_G{nb}', False)
print(cpt)
self.assertEqual(cpt,0)
def test_new_gen(self): #OK
nb_ped = 1
nb_people = [50]
nb_Gen_Max = [4]
nb_Gen_Min = [math.ceil(x/2) for x in nb_Gen_Max]
cl = 3
ped1 = Pedigree()
ped1.load("../data/ped/senegal2013.ped")
bn_sen = pview.ped_to_bn_compact(ped1,0.05)
print('clique sen',pview.max_clique_size(bn_sen))
print('uho', ped1.all_consanguineous_ped(cl))
for p, g_max, g_min in zip(nb_people, nb_Gen_Max, nb_Gen_Min):
for nb in range(nb_ped):
nbChild = random.randint(4, 8)
g = random.randint(g_min, g_max)
ped = Pedigree()
ped.gen_ped(nb, p, g, nbChild, cl)
# print('-------------------------')
# print(ped)
print('-------------------------')
print('Consanguin',ped.all_consanguineous_ped(cl))
bn = pview.ped_to_bn_compact(ped,0.05)
print('clique',pview.max_clique_size(bn))
print('-------------------------')
pview.save(ped, f'../pedigree_{p}_{g}_{nbChild}_{cl-1}_G{nb}')
pview.graph(ped, f'../generate_graph_{p}_{g}_{nbChild}_{cl-1}_G{nb}', False)
def test_graph(self): #OK
ped3 = Pedigree()
ped3.load("../data/ped/senegal2013.ped")
N8 = ped3.gen_family_pedigree('N8')
N8.add_sex_all()
N8.update_children_all()
N8.update_parents_all()
pview.graph(N8,"N8", False)
fam9 = Pedigree()
fam9.load("../data/ped/fam9.ped")
fam9.add_sex_all()
fam9.update_children_all()
fam9.update_parents_all()
pview.graph(fam9,"fam9", False)
N1 = ped3.gen_family_pedigree('N1')
N1.add_sex_all()
N1.update_children_all()
N1.update_parents_all()
pview.graph(N1,"N1", True)
def test_graph(self):
ped = Pedigree()
ped.load("../data/ped/famRh.ped")
ped.add_sex_all()
pview.graph(ped, 'famRh', False)
def blabla(self):
ped = Pedigree()
ped.load('../cplex/samples/IS/pedigree_10_3_7_3_G2.ped')
pview.graph(ped,generate,True)
def test_check_pedigree(self): #OK
ped = Pedigree()
ped.gen_ped('f', 2000, 10, 6, 3)
pview.graph(ped, f'../jpp', True)
print(ped)
def main(args=None):
"""
[--ped pedfile: format famid, id, patid (0 for founder), matid (0 for founder), gender (1 male, 2 female)
[--ev evidencefile]: format famid, id, ev00, ev10 (1 paternal), ev01 (1 maternal), ev11
[--famID Input the famID]
[--freq minorallelefreq (default: freq=0.01)]
[--targets list_of_ind (default: all)]
[--size] size of the rendered graph
[--bndot dotfile] export the BN into a dot file
[--peddot dotfile] export the pedigree into a dot file
[--audit textfile] introspect pedigree into a text file
[--verbose] display error/warning messages in stderr
[--mode] decide which version between normal, compact and multi version of a BN
[--thetha] format [probability, probability, ...]
[--centimorgans] format [distance, distance, ...]
[--inference ] Decide which inference use, LazyPropagation or LoobyBeliefPropagation
[--complete Bool] Decice which version between complete and compact for the audit file
[--out outfile] export probabilities into a out file
[--name_gen] format [str ,str ,str ...]
"""
parser = OptionParser(version="%prog 0.1",
usage="usage: %prog [options] pedfile")
parser.add_option("",
"--ev",
dest="evfile",
help="Specification of the profile",
metavar="FILE")
parser.add_option("",
"--freq",
dest="f",
help="minor allel freq (gamma)",
type="float",
default=0.01)
parser.add_option("", "--famID", dest='famID', help="Input the famID")
parser.add_option(
"",
"--targets",
dest="targets",
help="Specification of a list of targets (comma separated)")
parser.add_option("",
"--bndot",
dest="bndotfile",
help="Export the BN into a dot file",
metavar="FILE")
parser.add_option("",
"--peddot",
dest="peddotfile",
help="Export the pedigree into a dot file",
metavar="FILE")
parser.add_option("",
"--audit",
dest="auditfile",
help="Export some stats on pedigree in a text file",
metavar="FILE")
parser.add_option("",
"--verbose",
dest="verbose",
help="messages while processing",
default=False,
action="store_true")
parser.add_option("",
"--bn",
dest="bnfile",
help="Export the BN into a BIF file",
metavar="FILE")
parser.add_option(
"",
"--mode",
dest="mode",
help="Choose the type of the generate bn, compact, no compact or multi",
default='compact')
parser.add_option(
"",
"--theta",
dest="theta",
type="string",
help="Input a probability's distribution, shape: float;float; ...")
parser.add_option(
"",
"--centimorgans",
dest="centimorgans",
type="string",
help=
"Input the distance between genes in centimorgans, shape: float;float; ..."
)
parser.add_option("",
"--inference",
dest="inference",
help="Choose between LP and LBP",
default='LP')
parser.add_option(
"",
"--complete",
dest="complete",
help="Decide if the audit is a complete version or a compact version")
parser.add_option("",
"--out",
dest="out",
help="Export the evidence into a out file",
metavar="FILE")
parser.add_option("",
"--size",
dest="size",
help="Choose the size of the rendered graph",
type="int",
default=100)
parser.add_option("",
"--name_gen",
dest="name_gen",
type="string",
help="Input the gene's name, shape: str;str; ...")
if args is None:
(options, arguments) = parser.parse_args()
else:
(options, arguments) = parser.parse_args(args)
if len(arguments) != 2: # si on n'a pas mis de pedfile ou on en a mis trop
parser.parse_args(["--help"])
else:
# on retrouve toutes les valeurs dans options (principalement)
# options.peddotfile contient le nom du fichier
# options.verbose contient True or False
# etc.
print("=" * 40)
print(f"arguments: {arguments}")
print("=" * 40)
print(f"options: {options}")
print("=" * 40)
print("\n\n")
pedfile = arguments[1]
print(f"working on file : {pedfile}")
current_ped = ped.Pedigree()
current_ped.load(str(pedfile))
if options.famID:
famID = options.famID
else:
list_famID = current_ped.get_domain()
if len(list_famID) == 1:
famID = list_famID.pop()
else:
return "missing famID"
name_gen = None
if options.name_gen:
name_gen = options.name_gen.split(';')
print(name_gen)
if options.mode == 'compact':
bn = pview.ped_to_bn_compact(current_ped, options.f)
if options.verbose:
pview.gnb.showBN(bn, options.size)
elif options.mode == 'no_compact':
bn = pview.ped_to_bn(current_ped, options.f)
if options.verbose:
pview.gnb.showBN(bn, options.size)
elif options.mode == 'multi':
if options.theta:
distance = options.theta.split(';')
nb_gen = len(distance) + 1
for i in range(len(distance)):
distance[i] = float(distance[i])
bn = pview.bn_multi_pb(current_ped, options.f, nb_gen,
distance, name_gen)
if options.verbose:
pview.gnb.showBN(bn, options.size)
elif options.centimorgans:
centimorgans = options.centimorgans.split(';')
nb_gen = len(centimorgans)
for i in range(len(centimorgans)):
centimorgans[i] = float(centimorgans[i])
bn = pview.bn_multi_morgans(current_ped, options.f, nb_gen,
centimorgans, name_gen)
if options.verbose:
pview.gnb.showBN(bn, options.size)
else:
return "missing theta or centimorgan argument, cannot use the multi mode"
if options.bnfile:
bn.saveBIF(options.bndotfile)
pview.gum.availableBNExts()
pview.gum.saveBN(bn, options.bndotfile)
if options.verbose:
print('bndotfile saved in ' + options.bndotfile)
if options.bndotfile:
pview.save_dot(bn, options.bndotfile)
if options.verbose:
print('bn saved in ' + options.bndotfile)
if options.peddotfile:
if (len(current_ped)) > 1000:
pview.graph(current_ped, options.peddotfile, True)
else:
pview.graph(current_ped, options.peddotfile, False)
if options.verbose:
print("graph save in " + options.peddotfile)
if options.auditfile:
if options.complete == str(False):
print('false')
current_ped.pedigree_overview_file(options.auditfile, False)
else:
current_ped.pedigree_overview_file(options.auditfile, True)
if options.verbose:
print('audit file ' + options.auditfile + ' created')
if options.targets:
if options.evfile:
if options.mode == 'multi':
evidence = pview.load_evidence_multi(options.evfile, famID)
else:
evidence = pview.load_evidence(options.evfile, famID)
if options.verbose:
print(f"{options.evfile} loaded")
if options.inference == 'LBP':
ie = pview.gum.LoopyBeliefPropagation(bn)
else:
ie = pview.gum.LazyPropagation(bn)
ie.setEvidence(evidence)
ie.makeInference()
for i in current_ped.get_pedigree().keys():
if i in options.targets:
print(ie.posterior(f"X{i}"))
pview.create_out(options.out, current_ped, ie)
else:
if options.inference == 'LBP':
ie = pview.gum.LoopyBeliefPropagation(bn)
else:
ie = pview.gum.LazyPropagation(bn)
ie.makeInference()
for i in current_ped.get_pedigree().keys():
if i in options.targets:
print(ie.posterior(f"X{i}"))
pview.create_out(options.out, current_ped, ie)
else:
if options.evfile:
if options.mode == 'multi':
evidence = pview.load_evidence_multi(options.evfile, famID)
else:
evidence = pview.load_evidence(options.evfile, famID)
if options.verbose:
print(f"{options.evfile} loaded")
if options.inference == 'LBP':
ie = pview.gum.LoopyBeliefPropagation(bn)
else:
ie = pview.gum.LazyPropagation(bn)
ie.setEvidence(evidence)
ie.makeInference()
if options.mode == 'multi':
pview.create_out_multi(options.out, current_ped, ie,
nb_gen, name_gen)
else:
pview.create_out(options.out, current_ped, ie)
else:
if options.inference == 'LBP':
ie = pview.gum.LoopyBeliefPropagation(bn)
else:
ie = pview.gum.LazyPropagation(bn)
ie.makeInference()
if options.mode == 'multi':
pview.create_out_multi(options.out, current_ped, ie,
nb_gen, name_gen)
else:
pview.create_out(options.out, current_ped, ie)