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generateDataset.py
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"""
Generate the synthetic dataset used for the motif finding.
python generateDataset.py
@Chuankai Zhao, [email protected]
@Zheyi Zhu, Qingqing Zhang
"""
import numpy as np
import random
import os
# Genearte random sequences
def generate_sequences(SL, SC):
rd_seq = []
for i in range(SC):
rd_seq.append(''.join(random.choice("ACGT") for i in range(SL)))
return rd_seq
# Generate ICPC Matrix with given ICPC value
def genarate_ICPC_Matrix(ICPC):
ICPC_Matrix = []
if ICPC == 1.0:
p = 0.8105
elif ICPC == 1.5:
p = 0.9245
elif ICPC == 2.0:
p = 1.0
q = (1-p)/3
for i in range(0, 4):
newLine = []
for j in range(0, 4):
if j == i:
newLine.append(p)
else:
newLine.append(q)
ICPC_Matrix.append(newLine)
return ICPC_Matrix
# Generate random motif_matrix and motif_string
def generate_motifs(ICPC, ML, SC):
# @matrix_matrix: sum of ACGT values at each position with length ML
# @matrix_string: collection of random motif strings with size SC
BASE = ["A", "C", "G", "T"]
ICPC_Matrix = genarate_ICPC_Matrix(ICPC)
motif_matrix = [[0 for m in range(4)] for n in range(ML)]
motif_string = ["" for i in range(SC)]
for i in range(ML):
idx = random.randint(0,3)
probList = ICPC_Matrix[idx]
for j in range(SC):
# Random generate one char with ICPC distribution
motif_char_list = np.random.choice(BASE, 1, p = probList)
motif_char = motif_char_list[0]
motif_string[j] += motif_char
if motif_char == "A":
motif_matrix[i][0] += 1
elif motif_char == "C":
motif_matrix[i][1] += 1
elif motif_char == "G":
motif_matrix[i][2] += 1
elif motif_char == "T":
motif_matrix[i][3] += 1
return motif_matrix, motif_string
def generate_binding_site(SC, SL, ML):
binding_sites = []
for i in range(SC):
binding_sites.append(random.randint(0, SL-ML))
return binding_sites
def generate_planted_sequences(ICPC, ML, SL, SC):
new_rd_seq = []
rd_seq = generate_sequences(SL, SC)
binding_sites = generate_binding_site(SC, SL, ML)
motif_matrix, motif_string = generate_motifs(ICPC, ML, SC)
for i in range(SC):
new_seq_line = ""
start = binding_sites[i]
new_seq_line = rd_seq[i][:start] + motif_string[i] + rd_seq[i][start+ML:]
new_rd_seq.append(new_seq_line)
return new_rd_seq, binding_sites, motif_matrix
def write_to_file(dataset_dir, binding_sites, new_rd_seq, motif_matrix, ML):
seqs_dir = dataset_dir + '/sequences.fa'
f = open(seqs_dir, 'w')
for i in range(len(new_rd_seq)):
f.write('>sequence' + str(i+1) + '\n')
f.write(new_rd_seq[i])
f.write("\n")
f.close()
sites_dir = dataset_dir + '/sites.txt'
f = open(sites_dir, 'w')
for i in range(len(binding_sites)):
#f.write('>site' + str(i+1) + '\n')
f.write(str(binding_sites[i]))
f.write("\n")
f.close()
motif_dir = dataset_dir + '/motif.txt'
f = open(motif_dir, 'w')
f.write('>motif\t' + str(ML) + '\n')
for i in range(len(motif_matrix)):
f.write('\t'.join(map(str, motif_matrix[i])))
f.write("\n")
f.write("<\n")
f.close()
ml_dir = dataset_dir + '/motiflength.txt'
f = open(ml_dir, 'w')
f.write(str(ML))
f.close()
def main():
ICPC = 2
ML = 8
SL = 500
SC = 10
ICPC_list = [1, 1.5]
ML_list = [6, 7]
SC_list = [5, 20]
sl = SL
num_dataset = 10
datasets_directory = "./datasets/"
for icpc in ICPC_list:
ml = ML
sc = SC
for i in range(num_dataset):
dataset_directory = datasets_directory + "dataset_" + str(icpc) + "_" + str(ml) + "_" + str(sl) + "_" + str(sc) + "_" + str(i)
if not os.path.exists(dataset_directory):
os.makedirs(dataset_directory)
new_rd_seq, binding_sites, motif_matrix = generate_planted_sequences(icpc, ml, sl, sc)
write_to_file(dataset_directory, binding_sites, new_rd_seq, motif_matrix, ml)
for ml in ML_list:
icpc = ICPC
sc = SC
for i in range(num_dataset):
dataset_directory = datasets_directory + "dataset_" + str(icpc) + "_" + str(ml) + "_" + str(sl) + "_" + str(sc) + "_" + str(i)
if not os.path.exists(dataset_directory):
os.makedirs(dataset_directory)
new_rd_seq, binding_sites, motif_matrix = generate_planted_sequences(icpc, ml, sl, sc)
write_to_file(dataset_directory, binding_sites, new_rd_seq, motif_matrix, ml)
for sc in SC_list:
icpc = ICPC
ml = ML
for i in range(num_dataset):
dataset_directory = datasets_directory + "dataset_" + str(icpc) + "_" + str(ml) + "_" + str(sl) + "_" + str(sc) + "_" + str(i)
if not os.path.exists(dataset_directory):
os.makedirs(dataset_directory)
new_rd_seq, binding_sites, motif_matrix = generate_planted_sequences(icpc, ml, sl, sc)
write_to_file(dataset_directory, binding_sites, new_rd_seq, motif_matrix, ml)
icpc = ICPC
ml = ML
sc = SC
for i in range(num_dataset):
dataset_directory = datasets_directory + "dataset_" + str(icpc) + "_" + str(ml) + "_" + str(sl) + "_" + str(sc) + "_" + str(i)
if not os.path.exists(dataset_directory):
os.makedirs(dataset_directory)
new_rd_seq, binding_sites, motif_matrix = generate_planted_sequences(icpc, ml, sl, sc)
write_to_file(dataset_directory, binding_sites, new_rd_seq, motif_matrix, ml)
if __name__ == '__main__':
main()