Lightning

#! /usr/bin/python3

# Purpose of this script is to take a vcf file as an input stream, and randomly

# unphase or delete positions in order to give something for phasing or

# imputation software to attempt to phase or impute. (Ultimately, that output

# gets graded for accuracy, thus benchmarking the software).

#

# While unphasing or deleting positions, a memo is kept of which positions

# are modified, so that you know which to grade later.

#

import os

import sys

import random

random.seed("Lily")

# Keep a record of the positions you've changed here

# Note that line number isn't worth tracking because beagle output will throw

# off the count.

#

fh = open("./changed_lines", "w")

linenumber = 0

# Strategy for getting GT from input vcf stream is to find occurence of final

# tab. The GT always appears after the final tab. So reverse string and find 

# first tab.

#

def get_gt_from_vcf_line(line):

    reversed = line[-1::-1]

    # Now we look for first tab

    first_tab = reversed.index("\t")

    last_tab = len(line) - first_tab

    gt = line[last_tab:last_tab+3]

    return gt, last_tab

for line in sys.stdin:

    linenumber += 1

    line = line.strip()

    if line[0] == "#":

        print(line)

    else:

        gt, pos = get_gt_from_vcf_line(line)

        # will trigger randomly about .5% of the time

        # ensures that positions to be test imputed are chosen randomly

        if random.randint(1,200) == 1:

            fh.write(str(linenumber) + "\t" + str(pos) + "\t" + str(gt) + "\n")

            gt = "./."

        print(line[:pos] + gt + line[pos+3:])

fh.close()