464 lines
18 KiB
Python
464 lines
18 KiB
Python
#!/usr/bin/env python3
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import os
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import sys
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def get_core_variants(infile, cn):
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core_vars = []
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for line in open(infile, "r"):
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line = line.strip()
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core_vars.append(line)
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core_vars = ";".join(sorted(core_vars))
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if int(cn) == 1:
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core_vars = core_vars.replace("~0/1", "~1/1")
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if os.stat(infile).st_size == 0:
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core_vars = "REF alleles for rs1057126 and rs15561 in GRCh38"
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return core_vars
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def get_all_vars_gt(infile_full_gt):
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all_vars_gt = []
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for line in open(infile_full_gt, "r"):
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line = line.strip()
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all_vars_gt.append(line)
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all_vars_gt = ";".join(sorted(all_vars_gt))
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return all_vars_gt
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def cand_snv_allele_calling(database, infile, infile_full, infile_full_gt, infile_spec, cn):
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f = open(infile_spec, "r")
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all_variants = []
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for line in open(infile_full, "r"):
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line.strip()
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all_variants.append(line)
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# all_variants = line.strip().split(";")
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# print(all_variants)
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if os.stat(infile).st_size == 0:
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cand_res = ['10.v1_10.v1']
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allele_res = "*10/*10"
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return ["".join(cand_res), allele_res];
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#print("\nSupporting variants")
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#print("\n" + "".join(all_variants))
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sys.exit()
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# core_variants = []
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# for line in open(infile, "r"):
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# line = line.strip()
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# core_variants.append(line)
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# core_variants = ";".join(sorted(core_variants))
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core_variants = get_core_variants(infile, cn)
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# if int(cn) == 1:
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# core_variants = core_variants.replace("~0/1", "~1/1")
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# else:
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# pass
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all_var_gt = []
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for line in open(infile_full_gt, "r"):
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line = line.strip()
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all_var_gt.append(line)
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dbs = []
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for line in open(database, "r"):
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line = line.strip().split("\t")
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dbs.append(line)
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soln_list1 = []
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soln_list2 = []
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for record in dbs:
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record_core_var = record[1].split(";")
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record_core_var = ";".join(sorted(record_core_var))
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if record_core_var == core_variants:
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diplo = record[0]
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full_dip = record[2]
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soln_list1.append(record[0])
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soln_list2.append(record[2])
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else:
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pass
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#return soln_list1
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#print("\nResult:")
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diff_alleles_check = False
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def chkList(lst):
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if len(lst) < 0 :
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diff_alleles_check = True
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diff_alleles_check = all(ele == lst[0] for ele in lst)
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if(diff_alleles_check):
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return("Equal")
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else:
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return("Not equal")
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if len(soln_list1) == 1:
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diplo = "".join(soln_list1)
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res1 = [i for i in range(len(diplo)) if diplo.startswith("_", i)]
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res2 = [i for i in range(len(diplo)) if diplo.startswith(".", i)]
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hap1 = "*" + str (diplo[:res2[0]])
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hap2 = "*" + str (diplo[res1[0]+1:res2[1]])
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allele_res = hap1 + "/" + hap2
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return [soln_list1, diplo, allele_res];
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#print ("\nSupporting variants:")
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#print ("\n" + core_variants + "\n")
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elif len(soln_list1) == 2:
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diplo1 = soln_list1[0]
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diplo2 = soln_list1[1]
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diplo1_supp_var = soln_list2[0].split(";")
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diplo2_supp_var = soln_list2[1].split(";")
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uniq_diplo1 = []
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uniq_diplo2 = []
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for i in all_variants:
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if i not in diplo1_supp_var:
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uniq_diplo1.append(i)
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if i not in diplo2_supp_var:
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uniq_diplo2.append(i)
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#print("\nUnique variants in soln 1: {}".format(len(uniq_diplo1)))
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#print("\nUnique variants in soln 2: {}".format(len(uniq_diplo2)))
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if len(uniq_diplo1) < len(uniq_diplo2):
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res1 = [i for i in range(len(diplo1)) if diplo1.startswith("_", i)]
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res2 = [i for i in range(len(diplo1)) if diplo1.startswith(".", i)]
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hap1 = "*" + str (diplo1[:res2[0]])
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hap2 = "*" + str (diplo1[res1[0]+1:res2[1]])
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allele_res = hap1 + "/" + hap2
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return [soln_list1, diplo1, allele_res];
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#print ("Supporting variants:")
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#print ("\n" + core_variants + "\n")
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elif len(uniq_diplo1) > len(uniq_diplo2):
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res1 = [i for i in range(len(diplo2)) if diplo2.startswith("_", i)]
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res2 = [i for i in range(len(diplo2)) if diplo2.startswith(".", i)]
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hap1 = "*" + str (diplo2[:res2[0]])
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hap2 = "*" + str (diplo2[res1[0]+1:res2[1]])
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allele_res = hap1 + "/" + hap2
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return [soln_list1, diplo2, allele_res];
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#print ("Supporting variants:")
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#print ("\n" + core_variants + "\n")
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# elif len(uniq_diplo1) == len(uniq_diplo2) and (diplo1 == "4.v11_74.v1" and diplo2 == "4.v12_1.v1"):
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# res1 = [i for i in range(len(diplo2)) if diplo2.startswith("_", i)]
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# res2 = [i for i in range(len(diplo2)) if diplo2.startswith(".", i)]
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# hap1 = "*" + str (diplo2[:res2[0]])
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# hap2 = "*" + str (diplo2[res1[0]+1:res2[1]])
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# allele_res = hap1 + "/" + hap2
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# return [soln_list1, diplo2, allele_res];
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# elif len(uniq_diplo1) == len(uniq_diplo2) and diplo2 == "41.v1_65.v1":
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# res1 = [i for i in range(len(diplo2)) if diplo2.startswith("_", i)]
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# res2 = [i for i in range(len(diplo2)) if diplo2.startswith(".", i)]
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# hap1 = "*" + str (diplo2[:res2[0]])
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# hap2 = "*" + str (diplo2[res1[0]+1:res2[1]])
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# allele_res = hap1 + "/" + hap2
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# return [soln_list1, diplo2, allele_res];
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#print ("Supporting variants:")
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#print ("\n" + core_variants + "\n")
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# elif len(uniq_diplo1) == len(uniq_diplo2) and (diplo1 == "4.v1_6.v1" and diplo2 == "4.v4_6.v2") :
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# res1 = [i for i in range(len(diplo1)) if diplo1.startswith("_", i)]
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# res2 = [i for i in range(len(diplo1)) if diplo1.startswith(".", i)]
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# hap1 = "*" + str (diplo1[:res2[0]])
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# hap2 = "*" + str (diplo1[res1[0]+1:res2[1]])
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# allele_res = hap1 + "/" + hap2
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# return [soln_list1, diplo1, allele_res];
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#print ("Supporting variants:")
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#print ("\n" + core_variants + "\n")
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else:
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tiebreak1 = []
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tiebreak2 = []
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tiebreak3 = []
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score = []
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for line in f:
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line = line.strip().split()
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#print(line)
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if line[2] == core_variants:
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tiebreak1.append(line[1])
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tiebreak2.append(line[3])
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tiebreak3.append(line[0])
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for full_dip in tiebreak2:
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diplo_supp_gt = full_dip.split(";")
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uniq_gt = []
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for i in all_var_gt:
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if i not in diplo_supp_gt:
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uniq_gt.append(i)
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score_dip = len(uniq_gt)
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score.append(score_dip)
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min_score = min(score)
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# print(score)
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# if chkList(score) == "Equal" and soln_list1[0] == "17.v1_4.v1":
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# elem = "17.v1_4.v1"
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# res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
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# res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
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# hap1 = "*" + str (elem[:res2[0]])
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# hap2 = "*" + str (elem[res1[0]+1:res2[1]])
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# result_dip = hap1 + "/" + hap2
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# return [soln_list1, elem, result_dip];
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if chkList(score) == "Equal":
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amb_soln_set = []
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for elem in soln_list1:
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res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
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res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
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hap1 = "*" + str (elem[:res2[0]])
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hap2 = "*" + str (elem[res1[0]+1:res2[1]])
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result_dip = hap1 + "/" + hap2
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amb_soln_set.append(result_dip)
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#elem_pos = tiebreak1.index(elem)
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#print ("Solution " + str(elem_pos) + ": " + result_dip)
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allele_res = " or ".join(amb_soln_set)
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return [soln_list1, allele_res];
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# elif score.count(min_score) > 1 and soln_list1[0] == "11.v1_2.v2":
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# elem = "11.v1_2.v2"
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# res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
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# res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
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# hap1 = "*" + str (elem[:res2[0]])
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# hap2 = "*" + str (elem[res1[0]+1:res2[1]])
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# result_dip = hap1 + "/" + hap2
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# return [soln_list1, elem, result_dip];
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elif score.count(min_score) > 1:
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index_scores = []
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amb_soln_set = []
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for i in score:
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if i == min_score:
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index_scores.append(score.index(i))
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alt_solns = []
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for j in index_scores:
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elem = tiebreak1[j]
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res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
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res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
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hap1 = "*" + str (elem[:res2[0]])
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hap2 = "*" + str (elem[res1[0]+1:res2[1]])
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result_dip = hap1 + "/" + hap2
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alt_solns.append(result_dip)
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if chkList(alt_solns) == "Equal":
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return[soln_list1, alt_solns[0]];
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else:
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alt_solns = sorted(alt_solns)
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amb_soln_set.append(alt_solns[0])
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amb_soln_set.append(alt_solns[-1])
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allele_res = " or ".join(amb_soln_set)
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return [soln_list1, allele_res];
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# amb_soln_set = []
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# temp_set = []
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# temp_set.append(tiebreak1[0])
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# temp_set.append(tiebreak1[-1])
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# for elem in temp_set:
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# res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
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# res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
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# hap1 = "*" + str (elem[:res2[0]])
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# hap2 = "*" + str (elem[res1[0]+1:res2[1]])
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# result_dip = hap1 + "/" + hap2
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# amb_soln_set.append(result_dip)
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#elem_pos = tiebreak1.index(elem)
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#print ("Solution " + str(elem_pos) + ": " + result_dip)
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# allele_res = " or ".join(amb_soln_set)
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# return [soln_list1, allele_res];
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#print ("\nSupporting core variants:")
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#print ("\n" + core_variants + "\n")
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else:
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minpos = score.index(min_score)
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best_diplo = tiebreak1[minpos]
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best_cand_haps = tiebreak3[minpos]
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res1 = [i for i in range(len(best_diplo)) if best_diplo.startswith("_", i)]
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res2 = [i for i in range(len(best_diplo)) if best_diplo.startswith(".", i)]
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hap1 = "*" + str (best_diplo[:res2[0]])
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hap2 = "*" + str (best_diplo[res1[0]+1:res2[1]])
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allele_res = hap1 + "/" + hap2
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return [soln_list1, best_cand_haps, allele_res];
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#print ("Supporting core variants:")
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#print ("\n" + core_variants + "\n")
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elif len(soln_list1) == 3:
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diplo1 = soln_list1[0]
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diplo2 = soln_list1[1]
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diplo3 = soln_list1[2]
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diplo1_supp_var = soln_list2[0].split(";")
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diplo2_supp_var = soln_list2[1].split(";")
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diplo3_supp_var = soln_list2[2].split(";")
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uniq_diplo1 = []
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uniq_diplo2 = []
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uniq_diplo3 = []
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for i in all_variants:
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if i not in diplo1_supp_var:
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uniq_diplo1.append(i)
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if i not in diplo2_supp_var:
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uniq_diplo2.append(i)
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if i not in diplo3_supp_var:
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uniq_diplo3.append(i)
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if len(uniq_diplo1) < len(uniq_diplo2) and len(uniq_diplo1) < len(uniq_diplo3):
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res1 = [i for i in range(len(diplo1)) if diplo1.startswith("_", i)]
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res2 = [i for i in range(len(diplo1)) if diplo1.startswith(".", i)]
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hap1 = "*" + str (diplo1[:res2[0]])
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hap2 = "*" + str (diplo1[res1[0]+1:res2[1]])
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allele_res = hap1 + "/" + hap2
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return [soln_list1, diplo1, allele_res];
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#print ("Supporting variants:")
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#print ("\n" + core_variants + "\n")
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elif len(uniq_diplo1) > len(uniq_diplo2) and len(uniq_diplo2) < len(uniq_diplo3):
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res1 = [i for i in range(len(diplo2)) if diplo2.startswith("_", i)]
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res2 = [i for i in range(len(diplo2)) if diplo2.startswith(".", i)]
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hap1 = "*" + str (diplo2[:res2[0]])
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hap2 = "*" + str (diplo2[res1[0]+1:res2[1]])
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allele_res = hap1 + "/" + hap2
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return [soln_list1, diplo2, allele_res]
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#print ("Supporting variants:")
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#print ("\n" + core_variants + "\n")
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elif len(uniq_diplo1) > len(uniq_diplo2) and len(uniq_diplo2) > len(uniq_diplo3):
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res1 = [i for i in range(len(diplo3)) if diplo3.startswith("_", i)]
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res2 = [i for i in range(len(diplo3)) if diplo3.startswith(".", i)]
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hap1 = "*" + str (diplo3[:res2[0]])
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hap2 = "*" + str (diplo3[res1[0]+1:res2[1]])
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allele_res = hap1 + "/" + hap2
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return [soln_list1, diplo3, allele_res]
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#print ("Supporting variants:")
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#print ("\n" + core_variants + "\n")
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# elif len(uniq_diplo1) == len(uniq_diplo2) == len(uniq_diplo3) and diplo3 == "39.v1_4.v4":
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# res1 = [i for i in range(len(diplo3)) if diplo3.startswith("_", i)]
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# res2 = [i for i in range(len(diplo3)) if diplo3.startswith(".", i)]
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# hap1 = "*" + str (diplo3[:res2[0]])
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# hap2 = "*" + str (diplo3[res1[0]+1:res2[1]])
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# allele_res = hap1 + "/" + hap2
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# return [soln_list1, diplo3, allele_res]
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#print ("Supporting variants:")
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#print ("\n" + core_variants + "\n")
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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)):
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tiebreak1 = []
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tiebreak2 = []
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tiebreak3 = []
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score = []
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for line in f:
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line = line.strip().split()
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#print(line)
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if line[2] == core_variants:
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tiebreak1.append(line[1])
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tiebreak2.append(line[3])
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tiebreak3.append(line[0])
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for full_dip in tiebreak2:
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diplo_supp_gt = full_dip.split(";")
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uniq_gt = []
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for i in all_var_gt:
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if i not in diplo_supp_gt:
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uniq_gt.append(i)
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score_dip = len(uniq_gt)
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score.append(score_dip)
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min_score = min(score)
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# print(score)
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if chkList(score) == "Equal":
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amb_soln_set = []
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for elem in tiebreak1:
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res1 = [i for i in range(len(elem)) if elem.startswith("_", i)]
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res2 = [i for i in range(len(elem)) if elem.startswith(".", i)]
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hap1 = "*" + str (elem[:res2[0]])
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hap2 = "*" + str (elem[res1[0]+1:res2[1]])
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result_dip = hap1 + "/" + hap2
|
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amb_soln_set.append(result_dip)
|
|
#elem_pos = tiebreak1.index(elem)
|
|
#print ("Solution " + str(elem_pos) + ": " + result_dip)
|
|
allele_res = " or ".join(amb_soln_set)
|
|
return [soln_list1, tiebreak1, allele_res];
|
|
#print ("\nSupporting core variants:")
|
|
#print ("\n" + core_variants + "\n")
|
|
|
|
|
|
elif score.count(min_score) > 1:
|
|
index_scores = []
|
|
amb_soln_set = []
|
|
|
|
for i in score:
|
|
if i == min_score:
|
|
index_scores.append(score.index(i))
|
|
|
|
alt_solns = []
|
|
for j in index_scores:
|
|
elem = tiebreak1[j]
|
|
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
|
|
alt_solns.append(result_dip)
|
|
|
|
if chkList(alt_solns) == "Equal":
|
|
return[soln_list1, alt_solns[0]];
|
|
else:
|
|
alt_solns = sorted(alt_solns)
|
|
amb_soln_set.append(alt_solns[0])
|
|
amb_soln_set.append(alt_solns[-1])
|
|
allele_res = " or ".join(amb_soln_set)
|
|
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")
|
|
|
|
|
|
|
|
#print("\nFull diplotype variants:")
|
|
#print("\n" + ";".join(all_var_gt))
|