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update_ref.py
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import os
import collections
from Bio import SeqIO
import argparse
def insertion_points(LEP_folder, REP_folder, contigs_fai):
f = open(contigs_fai, 'r')
contig_len = {}
for line in f.readlines():
line = line.split('\n')[0]
line = line.split('\t')
contig_len[line[0]] = int(line[1])
f.close()
contig_insertion = {}
files = os.listdir(LEP_folder)
for file in files:
f = open(LEP_folder + file, 'r')
sample_ID = file.split('.txt')[0]
for line in f.readlines():
line = line.split('\n')[0]
line = line.split('\t')
contig_ID = line[0] + '_' + sample_ID
length = contig_len[contig_ID]
if line[3] == "reverse":
map_len = 101 - int(line[8])
else:
map_len = int(line[9]) - 1
contig_insertion[contig_ID] = [int(line[7]) - 1, 1.0 * (int(line[9]) - int(line[8])) / length, length,map_len]
f.close()
files = os.listdir(REP_folder)
for file in files:
f = open(REP_folder + file, 'r')
sample_ID = file.split('.txt')[0]
for line in f.readlines():
line = line.split('\n')[0]
line = line.split('\t')
contig_ID = line[0] + '_' + sample_ID
length = contig_len[contig_ID]
if line[3] == "no_reverse":
map_len = 101 - int(line[8])
else:
map_len = int(line[9]) - 1
contig_insertion[contig_ID] = [int(line[6]) - 1, 1.0 * (int(line[9]) - int(line[8])) / length, length,map_len]
f.close()
return contig_insertion
def obtain_seq(LEP_cluster_folder, REP_cluster_folder, LEP_rep_folder, REP_rep_folder):
LEP_rep = collections.defaultdict(list)
LEP_cluster = collections.defaultdict(list)
REP_rep = collections.defaultdict(list)
REP_cluster = collections.defaultdict(list)
# cluster
files = os.listdir(LEP_cluster_folder)
for file in files:
name = file.split(".")[0]
for record in SeqIO.parse(LEP_cluster_folder + file, "fasta"):
LEP_cluster[name].append([record.id, str(record.seq)])
files = os.listdir(REP_cluster_folder)
for file in files:
name = file.split(".")[0]
for record in SeqIO.parse(REP_cluster_folder + file, "fasta"):
REP_cluster[name].append([record.id, str(record.seq)])
# rep
files = os.listdir(LEP_rep_folder)
for file in files:
name = file.split(".")[0]
for record in SeqIO.parse(LEP_rep_folder + file, "fasta"):
LEP_rep[name].append(str(record.seq))
files = os.listdir(REP_rep_folder)
for file in files:
name = file.split(".")[0]
for record in SeqIO.parse(REP_rep_folder + file, "fasta"):
REP_rep[name].append(str(record.seq))
return LEP_cluster, REP_cluster, LEP_rep, REP_rep
def move_SEP_contigs(file, LEP_cluster, REP_cluster, LEP_add, REP_add, delete_LEP, delete_REP):
f = open(file, 'r')
for line in f.readlines():
line = line.split('\n')[0]
line = line.split('\t')
rep = line[len(line) - 1].split('.')
if rep[len(rep) - 1] == 'l':
for number1 in range(len(LEP_cluster[line[0]])):
LEP_add[rep[0]].append([LEP_cluster[line[0]][number1][0], LEP_cluster[line[0]][number1][1]])
for number1 in range(len(REP_cluster[line[1]])):
LEP_add[rep[0]].append([REP_cluster[line[1]][number1][0], REP_cluster[line[1]][number1][1]])
elif rep[len(rep) - 1] == 'r':
for number1 in range(len(LEP_cluster[line[0]])):
REP_add[rep[0]].append([LEP_cluster[line[0]][number1][0], LEP_cluster[line[0]][number1][1]])
for number1 in range(len(REP_cluster[line[1]])):
REP_add[rep[0]].append([REP_cluster[line[1]][number1][0], REP_cluster[line[1]][number1][1]])
delete_LEP.add(line[0])
delete_REP.add(line[1])
f.close()
return LEP_add, REP_add, delete_LEP, delete_REP
def overlap_SEP(file, contig_insert_pos):
f = open(file, 'r')
move_LEP = set()
move_REP = set()
for line in f.readlines():
line = line.split('\n')[0]
line = line.split('\t')
seq1 = line[len(line) - 2] # LEP
seq2 = line[len(line) - 1] # REP
contig_ID = seq1 + "." + seq2
if int(contig_insert_pos[seq1][0]) > int(contig_insert_pos[seq2][0]):
if contig_insert_pos[seq1][1] < contig_insert_pos[seq2][1]:
move_LEP.add(contig_ID)
elif contig_insert_pos[seq1][1] > contig_insert_pos[seq2][1]:
move_REP.add(contig_ID)
else:
if contig_insert_pos[seq1][2] < contig_insert_pos[seq2][2]:
move_LEP.add(contig_ID)
elif contig_insert_pos[seq1][2] > contig_insert_pos[seq2][2]:
move_REP.add(contig_ID)
else:
if contig_insert_pos[seq1][3] < contig_insert_pos[seq2][3]:
move_LEP.add(contig_ID)
elif contig_insert_pos[seq1][3] > contig_insert_pos[seq2][3]:
move_REP.add(contig_ID)
f.close()
return move_LEP, move_REP
def check_BEP_contigs(file, move_LEP, move_REP, LEP_cluster, REP_cluster, delete_LEP, delete_REP, LEP_add, REP_add,LEP_rep, REP_rep, merged_contig_folder):
f = open(file, 'r')
BEP_add = collections.defaultdict(list)
for line in f.readlines():
line = line.split('\n')[0]
line = line.split('\t')
LEP_ID = line[len(line) - 2]
REP_ID = line[len(line) - 1]
rep = LEP_ID + "." + REP_ID
for record in SeqIO.parse(merged_contig_folder + rep + "/" + rep + '.fa', "fasta"):
sequence = str(record.seq)
if rep in move_LEP:
LEP_rep[rep] = [sequence]
for number1 in range(len(LEP_cluster[line[0]])):
LEP_add[rep].append([LEP_cluster[line[0]][number1][0], LEP_cluster[line[0]][number1][1]])
for number1 in range(len(REP_cluster[line[1]])):
LEP_add[rep].append([REP_cluster[line[1]][number1][0], REP_cluster[line[1]][number1][1]])
elif rep in move_REP:
REP_rep[rep] = [sequence]
for number1 in range(len(LEP_cluster[line[0]])):
REP_add[rep].append([LEP_cluster[line[0]][number1][0], LEP_cluster[line[0]][number1][1]])
for number1 in range(len(REP_cluster[line[1]])):
REP_add[rep].append([REP_cluster[line[1]][number1][0], REP_cluster[line[1]][number1][1]])
else:
for number1 in range(len(LEP_cluster[line[0]])):
BEP_add[rep].append([LEP_cluster[line[0]][number1][0], LEP_cluster[line[0]][number1][1]])
for number1 in range(len(REP_cluster[line[1]])):
BEP_add[rep].append([REP_cluster[line[1]][number1][0], REP_cluster[line[1]][number1][1]])
delete_LEP.add(line[0])
delete_REP.add(line[1])
f.close()
return BEP_add, LEP_rep, REP_rep, LEP_add, REP_add, delete_LEP, delete_REP
def reobtain_rep_cluster(LEP_cluster, REP_cluster, LEP_rep, REP_rep, BEP_add, LEP_add, REP_add, delete_LEP, delete_REP,
REP_rep_update_folder, REP_cluster_update_folder, LEP_rep_update_folder,
LEP_cluster_update_folder, BEP_rep_folder, BEP_cluster_folder, merged_contig_folder):
for key in REP_rep:
if key not in delete_REP:
right_rep_path = open(REP_rep_update_folder + '/' + key + '.fa', 'w')
right_cluster_path = open(REP_cluster_update_folder + '/' + key + '.fa', 'w')
right_rep_path.write('>' + key + '\n')
right_rep_path.write(REP_rep[key][0] + '\n')
for number in range(len(REP_cluster[key])):
right_cluster_path.write('>' + REP_cluster[key][number][0] + '\n')
right_cluster_path.write(REP_cluster[key][number][1] + '\n')
right_rep_path.close()
right_cluster_path.close()
for key in LEP_rep:
if key not in delete_LEP:
left_rep_path = open(LEP_rep_update_folder + '/' + key + '.fa', 'w')
left_cluster_path = open(LEP_cluster_update_folder + '/' + key + '.fa', 'w')
left_rep_path.write('>' + key + '\n')
left_rep_path.write(LEP_rep[key][0] + '\n')
for number in range(len(LEP_cluster[key])):
left_cluster_path.write('>' + LEP_cluster[key][number][0] + '\n')
left_cluster_path.write(LEP_cluster[key][number][1] + '\n')
left_cluster_path.close()
left_rep_path.close()
for key in REP_add:
right_rep_path = open(REP_rep_update_folder + '/' + key + '.fa', 'w')
right_cluster_path = open(REP_cluster_update_folder + '/' + key + '.fa', 'w')
right_rep_path.write('>' + key + '\n')
right_rep_path.write(REP_rep[key][0] + '\n')
for number in range(len(REP_add[key])):
right_cluster_path.write('>' + REP_add[key][number][0] + '\n')
right_cluster_path.write(REP_add[key][number][1] + '\n')
right_rep_path.close()
right_cluster_path.close()
for key in LEP_add:
left_rep_path = open(LEP_rep_update_folder + "/" + key + '.fa', 'w')
left_cluster_path = open(LEP_cluster_update_folder + "/" + key + '.fa', 'w')
left_rep_path.write('>' + key + '\n')
left_rep_path.write(LEP_rep[key][0] + '\n')
for number in range(len(LEP_add[key])):
left_cluster_path.write('>' + LEP_add[key][number][0] + '\n')
left_cluster_path.write(LEP_add[key][number][1] + '\n')
left_rep_path.close()
left_cluster_path.close()
# add 2EP contigs
for key in BEP_add:
both_rep_path = open(BEP_rep_folder + '/' + key + '.fa', 'w')
both_cluster_path = open(BEP_cluster_folder + '/' + key + '.fa', 'w')
for record in SeqIO.parse(merged_contig_folder + key + "/" + key + '.fa', "fasta"):
both_rep_path.write('>' + key + '\n')
both_rep_path.write(str(record.seq) + '\n')
for number in range(len(BEP_add[key])):
both_cluster_path.write('>' + BEP_add[key][number][0] + '\n')
both_cluster_path.write(BEP_add[key][number][1] + '\n')
both_cluster_path.close()
both_rep_path.close()
if __name__ == '__main__':
parser = argparse.ArgumentParser(
description="Update the placed representatives and corresponding clusters.")
parser.add_argument("--LEP_folder",help="the folder of LEP contigs' alignment information (step2.files from point6)", required=True, default=None)
parser.add_argument("--REP_folder", help="fthe folder of REP contigs' alignment information (step2.files from point6)", required=True, default=None)
parser.add_argument("--contigs_fai", help="folder of contig.fa.fai", required=True, default=None)
parser.add_argument("--LEP_cluster_folder", help="folder of LEP_contigs.fa", required=True, default=None)
parser.add_argument("--REP_cluster_folder", help="folder of REP_cluster.fa", required=True, default=None)
parser.add_argument("--LEP_rep_folder", help="folder of LEP_rep.fa", required=True, default=None)
parser.add_argument("--REP_rep_folder", help="folder of REP_rep.fa", required=True, default=None)
parser.add_argument("--align_folder", help="folder of alignment result", required=True, default=None)
parser.add_argument("--merged_contig_folder", help="Path of merge.fa generated by PopINS", required=True,default=None)
parser.add_argument("--LEP_rep_update_folder", help="Save folder of updated LEP_rep.fa", required=True, default=None)
parser.add_argument("--LEP_cluster_update_folder", help="Save folder of updated LEP_contigs.fa", required=True,default=None)
parser.add_argument("--REP_rep_update_folder", help="Save folder of updated REP_rep.fa", required=True,default=None)
parser.add_argument("--REP_cluster_update_folder", help="Save folder of updated REP_contigs.fa", required=True, default=None)
parser.add_argument("--BEP_rep_folder", help="folder of REP_rep.fa", required=True, default=None)
parser.add_argument("--BEP_cluster_folder", help="folder of BEP_contigs.fa", required=True, default=None)
FLAGS = parser.parse_args()
LEP_cluster, REP_cluster, LEP_rep, REP_rep = obtain_seq(LEP_cluster_folder=FLAGS.LEP_cluster_folder,
REP_cluster_folder=FLAGS.REP_cluster_folder,
LEP_rep_folder=FLAGS.LEP_rep_folder,
REP_rep_folder=FLAGS.REP_rep_folder)
alignment_files = ["final_identity.txt", "final_contained.txt", "final_part.txt"]
LEP_add = collections.defaultdict(list)
REP_add = collections.defaultdict(list)
delete_LEP = set()
delete_REP = set()
for file in alignment_files:
file_path = FLAGS.align_folder + file
LEP_add, REP_add, delete_LEP, delete_REP = move_SEP_contigs(file_path, LEP_cluster, REP_cluster, LEP_add,
REP_add, delete_LEP, delete_REP)
file = FLAGS.align_folder + "final_overlap.txt"
contig_insertion = insertion_points(LEP_folder=FLAGS.LEP_folder, REP_folder=FLAGS.REP_folder,
contigs_fai=FLAGS.contigs_fai)
move_LEP, move_REP = overlap_SEP(file, contig_insertion)
BEP_add, LEP_rep, REP_rep, LEP_add, REP_add, delete_LEP, delete_REP = check_BEP_contigs(file, move_LEP, move_REP,
LEP_cluster, REP_cluster,
delete_LEP, delete_REP,
LEP_add, REP_add, LEP_rep,
REP_rep,
merged_contig_folder=FLAGS.merged_contig_folder)
reobtain_rep_cluster(LEP_cluster, REP_cluster, LEP_rep, REP_rep, BEP_add, LEP_add, REP_add, delete_LEP, delete_REP,
REP_rep_update_folder=FLAGS.REP_rep_update_folder,
REP_cluster_update_folder=FLAGS.REP_cluster_update_folder,
LEP_rep_update_folder=FLAGS.LEP_rep_update_folder,
LEP_cluster_update_folder=FLAGS.LEP_cluster_update_folder, BEP_rep_folder=FLAGS.BEP_rep_folder,
BEP_cluster_folder=FLAGS.BEP_cluster_folder, merged_contig_folder=FLAGS.merged_contig_folder)