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insertRepeat.py
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import os
import random
import numpy as np
import argparse as ap
import json
parser = ap.ArgumentParser()
parser.add_argument('--name', help='Dir', default="simulated")
parser.add_argument('--L', type=int, default=400,
help="Length of repeats")
parser.add_argument('--C', type=int, default=25,
help="Copy number of repeats ")
args = parser.parse_args()
# args.name = args.name + '_L' + str(args.L) + '_C' + str(args.C)
def make_genome(fname, org):
genome = "".join(random.choices(["A", "T", "G", "C"], [0.25, 0.25, 0.25, 0.25], k=(5000000-(args.L*args.C*2))))
with open(fname.split(".")[0] + '_' + str(org) + ".fasta", "w+") as wf:
wf.write(fname.split(".")[0] + "\n")
wf.write(genome + "\n")
return genome
def make_repeats(fnameR, N, probs, lens, org):
Repeats = []
with open(fnameR.split(".")[0] + '_' + str(org) + ".fasta", "w+") as wf:
for i in range(N):
prob_i = probs[i]
len_i = lens[i]
r_i = "".join(random.choices(["A", "T", "G", "C"], prob_i, k=len_i))
wf.write(">" + str(i) + " " + fnameR.split(".")[0] + "_" + str(org) + "_" + str(i) + "\n")
wf.write(r_i + "\n")
Repeats.append(r_i)
return Repeats
def generate(len_, count, mingap):
n = count
limit = len_
mingap = mingap
slack = limit - mingap * (n - 1)
steps = random.randint(0, slack)
increments = np.hstack([np.ones((steps,)), np.zeros((n,))])
np.random.shuffle(increments)
locs = np.argwhere(increments == 0).flatten()
return np.cumsum(increments)[locs] + mingap * np.arange(0, n)
def insert_repeats(dir_, fnameR, genome, N_intra, Repeats_intra, copys_intra, N_inter, Repeats_inter, copy_inter, org):
L = len(genome)
N_copy = sum(copys_intra) + sum(copy_inter)
mingap = int(0.5 * L / (N_copy - 1))
pos_all = generate(len(genome), N_copy, mingap)
with open(os.path.join(dir_, dir_ + '_inserted_offset_Repeats' + "_" + str(org) + '.fasta'), "w+") as wf:
for i in range(N_intra):
c_i = copys_intra[i]
r_i = Repeats_intra[i]
random_indices_i = random.sample(range(len(pos_all)), c_i)
pos_i = [pos_all[i] for i in random_indices_i]
pos_all = [x for x in pos_all if x not in pos_i]
wf.write(">" + str(i) + " " + fnameR.split(".")[0] + "_intra_" + str(i) + "\n")
for k in pos_i:
k = int(k)
genome = genome[:k] + r_i + genome[k:]
wf.write(str(k) + "\n")
for j in range(N_inter):
c_j = copy_inter[j]
r_j = Repeats_inter[j]
random_indices_j = random.sample(range(len(pos_all)), c_j)
pos_j = [pos_all[i] for i in random_indices_j]
pos_all = [x for x in pos_all if x not in pos_j]
wf.write(">" + str(j + N_intra) + " " + fnameR.split(".")[0] + "_inter_" + str(j) + "\n")
for k in pos_j:
k = int(k)
genome = genome[:k] + r_j + genome[k:]
wf.write(str(k) + "\n")
return genome
os.chdir('Data')
try:
os.makedirs(args.name, exist_ok=True)
print("Directory '%s' created successfully" % args.name)
except OSError as error:
print("Directory '%s' can not be created" % args.name)
cl_args = os.path.join(args.name, "commandline_args.txt")
with open(cl_args, 'w+') as f:
json.dump(args.__dict__, f, indent=2)
fname = os.path.join(args.name, args.name + ".fasta")
fnameR_intra = os.path.join(args.name, args.name + "_intraRepeats.fasta")
fnameR_inter = os.path.join(args.name, args.name + "_interRepeats.fasta")
copys_intra = [[args.C],[args.C]]
copys_inter = [[args.C],[args.C]]
length_intra = [[args.L],[args.L]]
length_inter = [args.L]
probs_intra = [[0.2, 0.3, 0.3, 0.2], [0.4, 0.2, 0.3, 0.1]]
probs_inter = [[0.1, 0.3, 0.2, 0.4]]
Repeats_inter = make_repeats(fnameR_inter, 1, probs_inter, length_inter, 99)
with open(os.path.join(args.name, "ref_genome.fasta"), "w+") as wf:
for i in range(2):
genome_i = make_genome(fname, i)
Repeats_intra_i = make_repeats(fnameR_intra, 1, probs_intra, length_intra[i], i)
inserted_genome_i = insert_repeats(args.name, fnameR_intra, genome_i, 1, Repeats_intra_i,
copys_intra[i], 1, Repeats_inter, copys_inter[i], i)
with open(os.path.join(args.name, "ref_genome_" + str(i) + ".fasta"), "w+") as wf_2:
wf_2.write(">ref_genome_" + str(i) + "\n")
wf_2.write(inserted_genome_i + "\n")
wf.write(">ref_genome_" + str(i) + "\n")
wf.write(inserted_genome_i + "\n")