33 lines
683 B
Python
33 lines
683 B
Python
#!/usr/bin/env python
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# Script: sim_zygosity.py
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# Author: David Twesigomwe
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# Date modified: 15-Dec-2020
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# Purpose: This script simulates the zygosity of variants after concatenating 2 haplotype VCF files.
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# Usage: python3 sim_zygosity.py in_database.txt > output.txt
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import os
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import sys
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in_file = sys.argv[1]
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f = open (in_file, "r")
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for line in f:
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list1 = line.strip().split(";")
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new_list = []
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for i in list1:
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x = i + '~0/1'
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y = i + '~1/1'
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if x not in new_list:
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new_list.append(x)
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else:
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new_list = list(map(lambda st: str.replace(st, x, y), new_list))
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print(";".join(new_list))
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f.close()
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