import sys

import os

import vcf

import pandas as pd

import numpy as np

import csv

import time

import json

def subfinder(mylist, pattern):

    for i in range(len(mylist)):

        if mylist[i] == pattern[0] and mylist[i:i + len(pattern)] == pattern:

            return i, i + len(pattern)

def promoter_var_idx(p_idx, promoter, var_idx):

    pmt_var = promoter[p_idx]  # which promoter

    p_start, p_end = subfinder(var_idx, pmt_var)

    return p_start, p_end

# IDS:

labels_file = 'labes.csv'

labels_df = pd.read_csv(labels_file,index_col=0)

ids = labels_df.FID.tolist()

# read promoter table

with open('promoter1.csv', 'rb') as f:

    reader = csv.reader(f)

    promoter = list(reader)

# read used variant posotions

with open('all_ALS_var.txt','r') as f:

    var_idx = [i.replace('\n','') for i in f]

print "number of promoters", len(promoter)

for i in range(10,100):#(len(promoter)):

    num_pro = i

    print "Generating No.",num_pro," promoter in chr",22

    p_start,p_end = promoter_var_idx(num_pro,promoter,var_idx=var_idx)

    promoter_ind = {}

    for ind in ids:

        indiv_file = 'individual/'+str(ind)+'.txt'

        with open(indiv_file,'r') as f:

            ind_v = [i.replace('\n','') for i in f]

        promo = ind_v[p_start:p_end]

        promoter_ind[ind] = promo

    with open('promoters/chr22_'+str(num_pro)+'.json', 'w') as fp:

        json.dump(promoter_ind, fp)