79 lines
1.8 KiB
Python
79 lines
1.8 KiB
Python
#!/usr/bin/env python3
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import os
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import sys
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def get_backgroud_alleles(database, core_vars):
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dbs = []
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dbs_temp = []
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core_vars_list = core_vars.split(";")
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core_temp1 = core_vars_list[-1][:-4]
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core_temp2 = core_vars_list[0][:-4]
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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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for record in dbs:
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temp_rec = record[1]
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if core_temp1 and core_temp2 in temp_rec:
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dbs_temp.append(record)
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scores = []
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candidates = []
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cand_vars = []
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for elem in dbs_temp:
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candidates.append(elem[0])
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record_core_var = elem[1].split(";")
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cand_vars.append(record_core_var)
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counter = 0
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for i in record_core_var:
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if i in core_vars_list:
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counter += 3
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elif i[:-4] in core_vars:
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counter += 1
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else:
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counter += -2
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scores.append(counter)
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cand_diplos = []
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diplo_vars2 = []
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if len(scores) == 0:
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diplo1 = '1B.v1_1B.v1'
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allele_res = '*1B/*1B'
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else:
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max_score = max(scores)
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indices = [i for i, x in enumerate(scores) if x == max_score or x == max_score - 1]
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for i in indices:
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diplo = candidates[i]
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diplo_vars1 = len(cand_vars[i])
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cand_diplos.append(diplo)
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diplo_vars2.append(diplo_vars1)
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min_index = diplo_vars2.index(min(diplo_vars2))
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diplo1 = cand_diplos[min_index]
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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 [allele_res, diplo1];
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