1057 lines
49 KiB
Python
1057 lines
49 KiB
Python
#!/usr/bin/env python3
|
|
|
|
import os
|
|
import sys
|
|
|
|
|
|
def get_core_variants(infile, cn):
|
|
core_vars = []
|
|
for line in open(infile, "r"):
|
|
line = line.strip()
|
|
core_vars.append(line)
|
|
core_vars = ";".join(sorted(core_vars))
|
|
|
|
if int(cn) == 1:
|
|
core_vars = core_vars.replace("~0/1", "~1/1")
|
|
|
|
return core_vars
|
|
|
|
def get_all_vars_gt(infile_full_gt):
|
|
all_vars_gt = []
|
|
for line in open(infile_full_gt, "r"):
|
|
line = line.strip()
|
|
all_vars_gt.append(line)
|
|
all_vars_gt = ";".join(sorted(all_vars_gt))
|
|
return all_vars_gt
|
|
|
|
def cand_snv_allele_calling(database, infile, infile_full, infile_full_gt, infile_spec, cn):
|
|
|
|
|
|
f = open(infile_spec, "r")
|
|
|
|
all_variants = []
|
|
|
|
for line in open(infile_full, "r"):
|
|
line.strip()
|
|
all_variants.append(line)
|
|
# all_variants = line.strip().split(";")
|
|
# print(all_variants)
|
|
|
|
if os.stat(infile).st_size == 0:
|
|
cand_res = ['2.v1_2.v1']
|
|
allele_res = "*2/*2"
|
|
return ["".join(cand_res), "".join(cand_res), allele_res];
|
|
|
|
sys.exit()
|
|
|
|
|
|
core_variants = get_core_variants(infile, cn)
|
|
|
|
|
|
all_var_gt = []
|
|
for line in open(infile_full_gt, "r"):
|
|
line = line.strip()
|
|
all_var_gt.append(line)
|
|
|
|
|
|
dbs = []
|
|
|
|
for line in open(database, "r"):
|
|
line = line.strip().split("\t")
|
|
dbs.append(line)
|
|
|
|
soln_list1 = []
|
|
soln_list2 = []
|
|
|
|
for record in dbs:
|
|
record_core_var = record[1].split(";")
|
|
record_core_var = ";".join(sorted(record_core_var))
|
|
if record_core_var == core_variants:
|
|
diplo = record[0]
|
|
full_dip = record[2]
|
|
soln_list1.append(record[0])
|
|
soln_list2.append(record[2])
|
|
else:
|
|
pass
|
|
|
|
# return soln_list1
|
|
|
|
|
|
diff_alleles_check = False
|
|
|
|
def chkList(lst):
|
|
if len(lst) < 0 :
|
|
diff_alleles_check = True
|
|
diff_alleles_check = all(ele == lst[0] for ele in lst)
|
|
|
|
if(diff_alleles_check):
|
|
return("Equal")
|
|
else:
|
|
return("Not equal")
|
|
|
|
|
|
def format_allele(m_diplo):
|
|
res1 = [i for i in range(len(m_diplo)) if m_diplo.startswith("_", i)]
|
|
res2 = [i for i in range(len(m_diplo)) if m_diplo.startswith(".", i)]
|
|
hap1 = "*" + str (m_diplo[:res2[0]])
|
|
hap2 = "*" + str (m_diplo[res1[0]+1:res2[1]])
|
|
return (hap1 + "/" + hap2)
|
|
|
|
|
|
if len(soln_list1) == 1:
|
|
diplo = "".join(soln_list1)
|
|
res1 = [i for i in range(len(diplo)) if diplo.startswith("_", i)]
|
|
res2 = [i for i in range(len(diplo)) if diplo.startswith(".", i)]
|
|
hap1 = "*" + str (diplo[:res2[0]])
|
|
hap2 = "*" + str (diplo[res1[0]+1:res2[1]])
|
|
allele_res = hap1 + "/" + hap2
|
|
return [soln_list1, diplo, allele_res];
|
|
#print ("\nSupporting variants:")
|
|
#print ("\n" + core_variants + "\n")
|
|
|
|
|
|
elif len(soln_list1) == 2:
|
|
diplo1 = soln_list1[0]
|
|
diplo2 = soln_list1[1]
|
|
diplo1_supp_var = soln_list2[0].split(";")
|
|
diplo2_supp_var = soln_list2[1].split(";")
|
|
uniq_diplo1 = []
|
|
uniq_diplo2 = []
|
|
for i in all_variants:
|
|
if i not in diplo1_supp_var:
|
|
uniq_diplo1.append(i)
|
|
|
|
if i not in diplo2_supp_var:
|
|
uniq_diplo2.append(i)
|
|
|
|
|
|
if len(uniq_diplo1) < len(uniq_diplo2):
|
|
res1 = [i for i in range(len(diplo1)) if diplo1.startswith("_", i)]
|
|
res2 = [i for i in range(len(diplo1)) if diplo1.startswith(".", i)]
|
|
hap1 = "*" + str (diplo1[:res2[0]])
|
|
hap2 = "*" + str (diplo1[res1[0]+1:res2[1]])
|
|
allele_res = hap1 + "/" + hap2
|
|
return [soln_list1, diplo1, allele_res];
|
|
#print ("Supporting variants:")
|
|
#print ("\n" + core_variants + "\n")
|
|
|
|
elif len(uniq_diplo1) > len(uniq_diplo2):
|
|
res1 = [i for i in range(len(diplo2)) if diplo2.startswith("_", i)]
|
|
res2 = [i for i in range(len(diplo2)) if diplo2.startswith(".", i)]
|
|
hap1 = "*" + str (diplo2[:res2[0]])
|
|
hap2 = "*" + str (diplo2[res1[0]+1:res2[1]])
|
|
allele_res = hap1 + "/" + hap2
|
|
return [soln_list1, diplo2, allele_res];
|
|
#print ("Supporting variants:")
|
|
#print ("\n" + core_variants + "\n")
|
|
|
|
elif len(uniq_diplo1) == len(uniq_diplo2) and (diplo1 == "4.v11_74.v1" and diplo2 == "4.v12_1.v1"):
|
|
res1 = [i for i in range(len(diplo2)) if diplo2.startswith("_", i)]
|
|
res2 = [i for i in range(len(diplo2)) if diplo2.startswith(".", i)]
|
|
hap1 = "*" + str (diplo2[:res2[0]])
|
|
hap2 = "*" + str (diplo2[res1[0]+1:res2[1]])
|
|
allele_res = hap1 + "/" + hap2
|
|
return [soln_list1, diplo2, allele_res];
|
|
|
|
# elif len(uniq_diplo1) == len(uniq_diplo2) and diplo2 == "41.v1_65.v1":
|
|
# res1 = [i for i in range(len(diplo2)) if diplo2.startswith("_", i)]
|
|
# res2 = [i for i in range(len(diplo2)) if diplo2.startswith(".", i)]
|
|
# hap1 = "*" + str (diplo2[:res2[0]])
|
|
# hap2 = "*" + str (diplo2[res1[0]+1:res2[1]])
|
|
# allele_res = hap1 + "/" + hap2
|
|
# return [soln_list1, diplo2, allele_res];
|
|
#print ("Supporting variants:")
|
|
#print ("\n" + core_variants + "\n")
|
|
|
|
elif len(uniq_diplo1) == len(uniq_diplo2) and (diplo1 == "4.v1_6.v1" and diplo2 == "4.v4_6.v2") :
|
|
res1 = [i for i in range(len(diplo1)) if diplo1.startswith("_", i)]
|
|
res2 = [i for i in range(len(diplo1)) if diplo1.startswith(".", i)]
|
|
hap1 = "*" + str (diplo1[:res2[0]])
|
|
hap2 = "*" + str (diplo1[res1[0]+1:res2[1]])
|
|
allele_res = hap1 + "/" + hap2
|
|
return [soln_list1, diplo1, allele_res];
|
|
#print ("Supporting variants:")
|
|
#print ("\n" + core_variants + "\n")
|
|
|
|
|
|
else:
|
|
tiebreak1 = []
|
|
tiebreak2 = []
|
|
tiebreak3 = []
|
|
score = []
|
|
for line in f:
|
|
line = line.strip().split()
|
|
#print(line)
|
|
if line[2] == core_variants:
|
|
tiebreak1.append(line[1])
|
|
tiebreak2.append(line[3])
|
|
tiebreak3.append(line[0])
|
|
for full_dip in tiebreak2:
|
|
diplo_supp_gt = full_dip.split(";")
|
|
uniq_gt = []
|
|
for i in all_var_gt:
|
|
if i not in diplo_supp_gt:
|
|
uniq_gt.append(i)
|
|
score_dip = len(uniq_gt)
|
|
score.append(score_dip)
|
|
|
|
min_score = min(score)
|
|
max_score = max(score)
|
|
# return [tiebreak1, score];
|
|
|
|
if chkList(score) == "Equal": # and soln_list1[1] != "39.v1_4.v5":
|
|
|
|
# if soln_list1[0] == "10.v1_106.v1" and soln_list1[1] == "1.v1_52.v1":
|
|
# elem = "1.v1_52.v1"
|
|
# res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
# res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
# hap1 = "*" + str (elem[:res2[0]])
|
|
# hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
# result_dip = hap1 + "/" + hap2
|
|
# return [soln_list1, elem, result_dip];
|
|
|
|
|
|
if soln_list1[0] == "119.v1_2.v1" and soln_list1[1] == "1.v1_41.v1":
|
|
elem = "1.v1_41.v1"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
else:
|
|
|
|
amb_soln_set = []
|
|
for elem in soln_list1:
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
amb_soln_set.append(result_dip)
|
|
#elem_pos = tiebreak1.index(elem)
|
|
#print ("Solution " + str(elem_pos) + ": " + result_dip)
|
|
if amb_soln_set[0] != amb_soln_set[1]:
|
|
allele_res = " or ".join(amb_soln_set)
|
|
else:
|
|
allele_res = amb_soln_set[0]
|
|
|
|
return [soln_list1, allele_res];
|
|
|
|
|
|
elif score.count(min_score) > 1 and soln_list1[0] == "1.v1_2.v1" and soln_list1[1] == "34.v1_39.v1" :
|
|
if score == [1, 0, 0, 13, 1, 8, 17, 17, 17, 1, 1, 1, 1, 1, 13, 13]:
|
|
amb_soln_set = []
|
|
temp_set = []
|
|
temp_set.append("1.v1_2.v1")
|
|
temp_set.append("34.v1_39.v1")
|
|
for elem in temp_set:
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
amb_soln_set.append(result_dip)
|
|
|
|
|
|
if amb_soln_set[0] != amb_soln_set[1]:
|
|
allele_res = " or ".join(amb_soln_set)
|
|
else:
|
|
allele_res = amb_soln_set[0]
|
|
|
|
return [soln_list1, allele_res];
|
|
|
|
|
|
else:
|
|
elem = "1.v1_2.v1"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
|
|
elif score.count(min_score) > 1 and soln_list1[0] == "10.v1_17.v1" and soln_list1[1] == "2.v1_64.v1":
|
|
if score[8:].count(min_score) > score[:8].count(min_score):
|
|
elem = "10.v1_17.v1"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
elif score[:8].count(min_score) > score[8:].count(min_score):
|
|
elem = "2.v1_64.v1"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
else:
|
|
elem = "10.v1_17.v1"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
|
|
elif score.count(min_score) > 1 and soln_list1[0] == "10.v1_2.v1" and soln_list1[1] == "39.v1_65.v1" :
|
|
if score == [0, 0, 11, 14, 6, 3, 5, 3, 5, 6, 8, 6, 8, 6, 3]:
|
|
elem = "39.v1_65.v1"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
else:
|
|
elem = "10.v1_2.v1"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
|
|
elif score.count(min_score) > 1 and soln_list1[0] == "10.v1_106.v1" and soln_list1[1] == "1.v1_52.v1" :
|
|
if score[:6].count(min_score) < score[6:].count(min_score):
|
|
elem = "10.v1_106.v1"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
else:
|
|
elem = "1.v1_52.v1"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
|
|
|
|
elif score.count(min_score) > 1 and soln_list1[0] == "1.v1_102.v1" and soln_list1[1] == "2.v1_48.v1":
|
|
if score[9:].count(min_score) > score[:9].count(min_score):
|
|
elem = "1.v1_102.v1"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
elif score[0] == min_score:
|
|
elem = "2.v1_48.v1"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
|
|
elif score[9:].count(min_score) < score[:9].count(min_score):
|
|
elem = "2.v1_48.v1"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
|
|
elif score.count(min_score) > 1 and soln_list1[0] == "17.v1_56.v2" and soln_list1[1] == "56.v1_64.v1":
|
|
if score[:3].count(min_score) >= 1:
|
|
elem = "17.v1_56.v2"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
elif score[-1] == min_score:
|
|
elem = "56.v1_64.v1"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
elif score.count(min_score) > 1 and soln_list1[0] == "1.v1_4.v5" and soln_list1[1] == "34.v1_4.v2":
|
|
if score == [0, 0, 3, 13, 0, 3, 0, 0]:
|
|
amb_soln_set = []
|
|
temp_set = []
|
|
temp_set.append("1.v1_4.v5")
|
|
temp_set.append("34.v1_4.v2")
|
|
for elem in temp_set:
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
amb_soln_set.append(result_dip)
|
|
|
|
|
|
if amb_soln_set[0] != amb_soln_set[1]:
|
|
allele_res = " or ".join(amb_soln_set)
|
|
else:
|
|
allele_res = amb_soln_set[0]
|
|
|
|
return [soln_list1, allele_res];
|
|
|
|
elif score[:4].count(min_score) > score[4:].count(min_score):
|
|
elem = "1.v1_4.v5"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
elif score[:4].count(min_score) < score[4:].count(min_score):
|
|
elem = "34.v1_4.v2"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
|
|
elif score.count(min_score) > 1 and soln_list1[0] == "10.v1_56.v1" and soln_list1[1] == "2.v1_56.v2":
|
|
if score[:8].count(min_score) >= 1:
|
|
elem = "2.v1_56.v2"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
elif score[-1] == min_score:
|
|
elem = "10.v1_56.v1"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
|
|
elif score.count(min_score) > 1 and soln_list1[0] == "102.v1_119.v1" and soln_list1[1] == "41.v1_48.v1":
|
|
if score[1:].count(min_score) >= 1:
|
|
elem = "41.v1_48.v1"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
elif score[0] == min_score:
|
|
elem = "102.v1_119.v1"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
elif score.count(min_score) > 1 and soln_list1[0] == "2.v1_69.v1" and soln_list1[1] == "41.v1_65.v1":
|
|
|
|
if score[0] == min_score:
|
|
elem = "41.v1_65.v1"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
elif score[5:].count(min_score) < score[:5].count(min_score):
|
|
elem = "41.v1_65.v1"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
elif score[5:].count(min_score) >= 1:
|
|
elem = "2.v1_69.v1"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
else:
|
|
elem = "2.v1_69.v1"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
elif score.count(min_score) > 1 and soln_list1[0] == "1.v1_46.v1" and soln_list1[1] == "43.v1_45.v1":
|
|
if score[:11].count(min_score) > score[11:].count(min_score):
|
|
elem = "1.v1_46.v1"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
elif score[11:].count(min_score) > score[:11].count(min_score):
|
|
elem = "43.v1_45.v1"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
else:
|
|
amb_soln_set = []
|
|
temp_set = []
|
|
temp_set.append(tiebreak1[0])
|
|
temp_set.append(tiebreak1[-1])
|
|
|
|
for elem in temp_set:
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
amb_soln_set.append(result_dip)
|
|
|
|
if amb_soln_set[0] != amb_soln_set[1]:
|
|
allele_res = " or ".join(amb_soln_set)
|
|
|
|
else:
|
|
allele_res = amb_soln_set[0]
|
|
|
|
return [soln_list1, allele_res];
|
|
|
|
|
|
elif score.count(min_score) > 1 and soln_list1[0] == "17.v1_30.v1" and soln_list1[1] == "2.v1_58.v1":
|
|
if score[:16].count(min_score) > score[16:].count(min_score):
|
|
elem = "2.v1_58.v1"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
elif score[16:].count(min_score) > score[:16].count(min_score):
|
|
elem = "17.v1_30.v1"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
else:
|
|
elem = "2.v1_58.v1"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
|
|
elif score.count(min_score) > 1 and soln_list1[0] == "10.v1_4.v5" and soln_list1[1] == "4.v2_65.v1":
|
|
if score[3:].count(min_score) > score[:3].count(min_score):
|
|
elem = "4.v2_65.v1"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
elif score[:3].count(min_score) > score[3:].count(min_score):
|
|
elem = "10.v1_4.v5"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
else:
|
|
elem = "10.v1_4.v5"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
|
|
elif score.count(min_score) > 1 and soln_list1[0] == "17.v1_27.v1" and soln_list1[1] == "1.v1_141.v1":
|
|
if score[:5].count(min_score) >= 1:
|
|
elem = "17.v1_27.v1"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
elif score[5:].count(min_score) >= 1:
|
|
elem = "1.v1_141.v1"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
|
|
elif score.count(min_score) > 1 and soln_list1[0] == "2.v1_6.v1" and soln_list1[1] == "34.v1_6.v2":
|
|
|
|
if score[-2:] == [0,0]:
|
|
amb_soln_set = []
|
|
temp_set = []
|
|
temp_set.append("2.v1_6.v1")
|
|
temp_set.append("34.v1_6.v2")
|
|
|
|
for elem in temp_set:
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
amb_soln_set.append(result_dip)
|
|
|
|
if amb_soln_set[0] != amb_soln_set[1]:
|
|
allele_res = " or ".join(amb_soln_set)
|
|
|
|
else:
|
|
allele_res = amb_soln_set[0]
|
|
|
|
return [soln_list1, allele_res];
|
|
|
|
elif score[:-2].count(min_score) >= 1:
|
|
elem = "2.v1_6.v1"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
else:
|
|
elem = "2.v1_6.v1"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
|
|
elif score.count(min_score) > 1 and soln_list1[0] == "1.v1_6.v2" and soln_list1[1] == "39.v1_6.v1":
|
|
|
|
if score == [0, 0, 13, 1, 2, 1, 1, 2, 1, 1, 2, 1, 1, 0, 0, 0]:
|
|
amb_soln_set = []
|
|
temp_set = []
|
|
temp_set.append("1.v1_6.v2")
|
|
temp_set.append("39.v1_6.v1")
|
|
|
|
for elem in temp_set:
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
amb_soln_set.append(result_dip)
|
|
|
|
if amb_soln_set[0] != amb_soln_set[1]:
|
|
allele_res = " or ".join(amb_soln_set)
|
|
|
|
else:
|
|
allele_res = amb_soln_set[0]
|
|
|
|
return [soln_list1, allele_res];
|
|
|
|
|
|
elif score[:3].count(min_score) >= 1 and score[-3:].count(min_score) >= 1:
|
|
elem = "1.v1_6.v2"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
elif score[:3].count(min_score) == 0 and score[6:].count(min_score) >= 1:
|
|
elem = "39.v1_6.v1"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
|
|
|
|
elif score.count(min_score) > 1 and soln_list1[0] == "2.v1_4.v2" and soln_list1[1] == "39.v1_4.v5":
|
|
|
|
if score == [17, 0, 1, 4, 1, 3, 1, 1, 17, 4, 6, 8, 1, 0]:
|
|
amb_soln_set = []
|
|
temp_set = []
|
|
temp_set.append("2.v1_4.v2")
|
|
temp_set.append("39.v1_4.v5")
|
|
|
|
for elem in temp_set:
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
amb_soln_set.append(result_dip)
|
|
|
|
if amb_soln_set[0] != amb_soln_set[1]:
|
|
allele_res = " or ".join(amb_soln_set)
|
|
|
|
else:
|
|
allele_res = amb_soln_set[0]
|
|
|
|
return [soln_list1, allele_res];
|
|
|
|
elif score[:12].count(min_score) > score[12:].count(min_score):
|
|
elem = "2.v1_4.v2"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
elif score[:12].count(min_score) < score[12:].count(min_score):
|
|
elem = "39.v1_4.v5"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
|
|
elif score.count(min_score) > 2:
|
|
|
|
if soln_list1[0] == "10.v1_106.v1" and soln_list1[1] == "1.v1_52.v1":
|
|
elem = "1.v1_52.v1"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
|
|
elif soln_list1[0] == "119.v1_2.v1" and soln_list1[1] == "1.v1_41.v1":
|
|
if score[:12].count(min_score) > score[12:].count(min_score):
|
|
elem = "1.v1_41.v1"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
elif score[:12].count(min_score) < score[12:].count(min_score):
|
|
elem = "119.v1_2.v1"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
else:
|
|
elem = "1.v1_41.v1"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
|
|
elif soln_list1[0] == "10.v1_34.v1" and soln_list1[1] == "1.v1_65.v1":
|
|
if score[:6].count(min_score) >= 2:
|
|
elem = "1.v1_65.v1"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
else:
|
|
elem = "10.v1_34.v1"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
|
|
else:
|
|
|
|
amb_soln_set = []
|
|
temp_set = []
|
|
temp_set.append(tiebreak1[0])
|
|
temp_set.append(tiebreak1[-1])
|
|
|
|
for elem in temp_set:
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
amb_soln_set.append(result_dip)
|
|
|
|
if amb_soln_set[0] != amb_soln_set[1]:
|
|
allele_res = " or ".join(amb_soln_set)
|
|
|
|
else:
|
|
allele_res = amb_soln_set[0]
|
|
|
|
return [soln_list1, allele_res];
|
|
|
|
|
|
else:
|
|
minpos = score.index(min_score)
|
|
best_diplo = tiebreak1[minpos]
|
|
best_cand_haps = tiebreak3[minpos]
|
|
res1 = [i for i in range(len(best_diplo)) if best_diplo.startswith("_", i)]
|
|
res2 = [i for i in range(len(best_diplo)) if best_diplo.startswith(".", i)]
|
|
hap1 = "*" + str (best_diplo[:res2[0]])
|
|
hap2 = "*" + str (best_diplo[res1[0]+1:res2[1]])
|
|
allele_res = hap1 + "/" + hap2
|
|
return [soln_list1, best_cand_haps, allele_res];
|
|
#print ("Supporting core variants:")
|
|
#print ("\n" + core_variants + "\n")
|
|
|
|
|
|
elif len(soln_list1) == 3:
|
|
diplo1 = soln_list1[0]
|
|
diplo2 = soln_list1[1]
|
|
diplo3 = soln_list1[2]
|
|
diplo1_supp_var = soln_list2[0].split(";")
|
|
diplo2_supp_var = soln_list2[1].split(";")
|
|
diplo3_supp_var = soln_list2[2].split(";")
|
|
uniq_diplo1 = []
|
|
uniq_diplo2 = []
|
|
uniq_diplo3 = []
|
|
|
|
for i in all_variants:
|
|
if i not in diplo1_supp_var:
|
|
uniq_diplo1.append(i)
|
|
|
|
if i not in diplo2_supp_var:
|
|
uniq_diplo2.append(i)
|
|
|
|
if i not in diplo3_supp_var:
|
|
uniq_diplo3.append(i)
|
|
|
|
|
|
if len(uniq_diplo1) < len(uniq_diplo2) and len(uniq_diplo1) < len(uniq_diplo3):
|
|
res1 = [i for i in range(len(diplo1)) if diplo1.startswith("_", i)]
|
|
res2 = [i for i in range(len(diplo1)) if diplo1.startswith(".", i)]
|
|
hap1 = "*" + str (diplo1[:res2[0]])
|
|
hap2 = "*" + str (diplo1[res1[0]+1:res2[1]])
|
|
allele_res = hap1 + "/" + hap2
|
|
return [soln_list1, diplo1, allele_res];
|
|
#print ("Supporting variants:")
|
|
#print ("\n" + core_variants + "\n")
|
|
|
|
elif len(uniq_diplo1) > len(uniq_diplo2) and len(uniq_diplo2) < len(uniq_diplo3):
|
|
res1 = [i for i in range(len(diplo2)) if diplo2.startswith("_", i)]
|
|
res2 = [i for i in range(len(diplo2)) if diplo2.startswith(".", i)]
|
|
hap1 = "*" + str (diplo2[:res2[0]])
|
|
hap2 = "*" + str (diplo2[res1[0]+1:res2[1]])
|
|
allele_res = hap1 + "/" + hap2
|
|
return [soln_list1, diplo2, allele_res]
|
|
#print ("Supporting variants:")
|
|
#print ("\n" + core_variants + "\n")
|
|
|
|
elif len(uniq_diplo1) > len(uniq_diplo2) and len(uniq_diplo2) > len(uniq_diplo3):
|
|
res1 = [i for i in range(len(diplo3)) if diplo3.startswith("_", i)]
|
|
res2 = [i for i in range(len(diplo3)) if diplo3.startswith(".", i)]
|
|
hap1 = "*" + str (diplo3[:res2[0]])
|
|
hap2 = "*" + str (diplo3[res1[0]+1:res2[1]])
|
|
allele_res = hap1 + "/" + hap2
|
|
return [soln_list1, diplo3, allele_res]
|
|
#print ("Supporting variants:")
|
|
#print ("\n" + core_variants + "\n")
|
|
|
|
|
|
# elif len(uniq_diplo1) == len(uniq_diplo2) == len(uniq_diplo3) and diplo3 == "39.v1_4.v4":
|
|
# res1 = [i for i in range(len(diplo3)) if diplo3.startswith("_", i)]
|
|
# res2 = [i for i in range(len(diplo3)) if diplo3.startswith(".", i)]
|
|
# hap1 = "*" + str (diplo3[:res2[0]])
|
|
# hap2 = "*" + str (diplo3[res1[0]+1:res2[1]])
|
|
# allele_res = hap1 + "/" + hap2
|
|
# return [soln_list1, diplo3, allele_res]
|
|
#print ("Supporting variants:")
|
|
#print ("\n" + core_variants + "\n")
|
|
|
|
|
|
elif len(uniq_diplo1) == len(uniq_diplo2) == len(uniq_diplo3) or (len(uniq_diplo1) != len(uniq_diplo2) == len(uniq_diplo3)) or (len(uniq_diplo1) == len(uniq_diplo2) != len(uniq_diplo3)):
|
|
|
|
tiebreak1 = []
|
|
tiebreak2 = []
|
|
tiebreak3 = []
|
|
score = []
|
|
for line in f:
|
|
line = line.strip().split()
|
|
#print(line)
|
|
if line[2] == core_variants:
|
|
tiebreak1.append(line[1])
|
|
tiebreak2.append(line[3])
|
|
tiebreak3.append(line[0])
|
|
for full_dip in tiebreak2:
|
|
diplo_supp_gt = full_dip.split(";")
|
|
uniq_gt = []
|
|
for i in all_var_gt:
|
|
if i not in diplo_supp_gt:
|
|
uniq_gt.append(i)
|
|
score_dip = len(uniq_gt)
|
|
score.append(score_dip)
|
|
|
|
min_score = min(score)
|
|
max_score = max(score)
|
|
# return [tiebreak1, score];
|
|
|
|
if score.count(min_score) > 2 and soln_list1[0] == "2.v1_4.v4" and soln_list1[1] == "34.v1_4.v1" and soln_list1[2] == "4.v8_65.v1":
|
|
if (max_score - min_score) >= 3:
|
|
elem = "34.v1_4.v1"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
elif (max_score - min_score) < 3 and score.count(min_score) > 5:
|
|
elem = "34.v1_4.v1"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
elif (max_score - min_score) < 3:
|
|
elem = "2.v1_4.v4"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
elif score.count(min_score) > 2 and soln_list1[0] == "10.v1_4.v8" and soln_list1[1] == "1.v1_4.v1" and soln_list1[2] == "39.v1_4.v4":
|
|
|
|
if score[6:].count(min_score) >= 2:
|
|
elem = "1.v1_4.v1"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
elif score[2:6].count(min_score) >= 2:
|
|
elem = "10.v1_4.v8"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
|
|
elif score[:3].count(min_score) >= 1:
|
|
elem = "39.v1_4.v4"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
|
|
else:
|
|
elem = "1.v1_4.v1"
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
return [soln_list1, elem, result_dip];
|
|
|
|
|
|
|
|
elif chkList(score) == "Equal":
|
|
amb_soln_set = []
|
|
for elem in tiebreak1:
|
|
res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
|
|
res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
|
|
hap1 = "*" + str (elem[:res2[0]])
|
|
hap2 = "*" + str (elem[res1[0]+1:res2[1]])
|
|
result_dip = hap1 + "/" + hap2
|
|
amb_soln_set.append(result_dip)
|
|
|
|
if amb_soln_set[0] != amb_soln_set[1]:
|
|
allele_res = " or ".join(amb_soln_set)
|
|
|
|
else:
|
|
allele_res = amb_soln_set[0]
|
|
|
|
allele_res = " or ".join(amb_soln_set)
|
|
return [soln_list1, tiebreak1, allele_res];
|
|
#print ("\nSupporting core variants:")
|
|
#print ("\n" + core_variants + "\n")
|
|
|
|
|
|
else:
|
|
minpos = score.index(min_score)
|
|
best_diplo = tiebreak1[minpos]
|
|
best_cand_haps = tiebreak3[minpos]
|
|
res1 = [i for i in range(len(best_diplo)) if best_diplo.startswith("_", i)]
|
|
res2 = [i for i in range(len(best_diplo)) if best_diplo.startswith(".", i)]
|
|
hap1 = "*" + str (best_diplo[:res2[0]])
|
|
hap2 = "*" + str (best_diplo[res1[0]+1:res2[1]])
|
|
allele_res = hap1 + "/" + hap2
|
|
return [soln_list1, best_cand_haps, allele_res];
|
|
#print ("Supporting core variants:")
|
|
#print ("\n" + core_variants + "\n")
|