/
dedup.py
executable file
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dedup.py
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#!/usr/bin/python
#-*- coding: UTF-8 -*-
import os
import sys
from optparse import OptionParser
import pysam
import time
import multiprocessing
def parseCommand():
usage = "usage: ./dedup.py -1 in.sorted.bam -o out.bam > dedup.log"
version = "%prog 1.0"
parser = OptionParser(usage=usage, version=version)
parser.add_option("-1", "--input1", dest="input1", help="the bam file")
parser.add_option("-q", "--phredQ", dest="phred",
help="Phred quality score threshold", type="int", default="20")
parser.add_option("-o", "--output", dest="output",
default=".", help="output file".decode("utf8"))
return parser.parse_args()
def str_compare(forward_list1, forward_list2, reverse_list1, reverse_list2, phredQ=20):
seq_1 = forward_list1[2] + reverse_list1[2]
phred_1 = forward_list1[3].tolist()
tmp_2 = reverse_list1[3].tolist()
phred_1.extend(tmp_2)
seq_2 = forward_list2[2] + reverse_list2[2]
phred_2 = forward_list2[3].tolist()
tmp_2 = reverse_list2[3].tolist()
phred_2.extend(tmp_2)
if len(seq_1) == len(seq_2):
if seq_1 == seq_2:
return True
else:
index = [0]
count = 0
for i in range(len(seq_1)):
if phred_1[i] < phredQ or phred_2[i] < phredQ:
if i == 0:
if seq_1[i] != seq_2[i]:
return False
else:
index.append(i)
count += 1
if seq_1[(index[count - 1] + 1):index[count]] != seq_2[(index[count - 1] + 1):index[count]]:
return False
else:
if seq_1[i] == seq_2[i]:
continue
else:
return False
return True
else:
return False
def block_compare(forward_block_dict_list, reverse_block_dict, phredQ=20):
dup_seqname_dict = {}
save_number_dict = {}
line_number_list = [save_number_dict, dup_seqname_dict]
start = True
for i in range(len(forward_block_dict_list)):
if forward_block_dict_list[i][1] not in dup_seqname_dict:
save_number_dict[forward_block_dict_list[i][0]] = True
if forward_block_dict_list[i][1] not in reverse_block_dict:
continue
for j in range((i + 1), len(forward_block_dict_list)):
if forward_block_dict_list[j][1] not in dup_seqname_dict:
if forward_block_dict_list[j][1] in reverse_block_dict:
if str_compare(forward_block_dict_list[i], forward_block_dict_list[j], reverse_block_dict[forward_block_dict_list[i][1]], reverse_block_dict[forward_block_dict_list[j][1]], phredQ):
dup_seqname_dict[forward_block_dict_list[j][1]] = True
return line_number_list
def dedup3(in_file, phred, out_file):
f = pysam.AlignmentFile(in_file, "rb")
total = 0
buffer_block = []
forward_block_dict = {}
reverse_block_dict = {}
other_dict = {}
chrom_flag = False
chrom_tmp = "chrM"
line_list = []
dedup_dict = {}
save_dict = {}
for frag in f:
if frag.is_proper_pair:
if frag.template_length > 0:
if frag.reference_id not in forward_block_dict:
forward_block_dict[frag.reference_id] = {}
forward_block_dict[frag.reference_id][frag.reference_start] = [
[total, frag.query_name, frag.query_sequence, frag.query_qualities]]
if not chrom_flag:
chrom_tmp = frag.reference_id
chrom_flag = True
total += 1
continue
for i in forward_block_dict[chrom_tmp].keys():
if len(forward_block_dict[chrom_tmp][i]) >= 2:
line_list = block_compare(forward_block_dict[chrom_tmp][
i], reverse_block_dict[chrom_tmp], phred)
dedup_dict.update(line_list[1])
save_dict.update(line_list[0])
else:
save_dict[forward_block_dict[
chrom_tmp][i][0][0]] = True
forward_block_dict[chrom_tmp].clear()
for i in reverse_block_dict[chrom_tmp].keys():
if i not in dedup_dict:
save_dict[reverse_block_dict[
chrom_tmp][i][0]] = True
reverse_block_dict[chrom_tmp].clear()
chrom_tmp = frag.reference_id
elif frag.reference_start not in forward_block_dict[frag.reference_id]:
forward_block_dict[frag.reference_id][
frag.reference_start] = {}
forward_block_dict[frag.reference_id][frag.reference_start] = [
[total, frag.query_name, frag.query_sequence, frag.query_qualities]]
else:
forward_block_dict[frag.reference_id][frag.reference_start].append(
[total, frag.query_name, frag.query_sequence, frag.query_qualities])
elif frag.template_length < 0:
if frag.reference_id not in reverse_block_dict:
reverse_block_dict[frag.reference_id] = {}
reverse_block_dict[frag.reference_id][frag.query_name] = [
total, frag.query_name, frag.query_sequence, frag.query_qualities]
else:
reverse_block_dict[frag.reference_id][frag.query_name] = [
total, frag.query_name, frag.query_sequence, frag.query_qualities]
else:
other_dict[total] = True
else:
other_dict[total] = True
total += 1
if chrom_tmp in forward_block_dict:
for i in forward_block_dict[chrom_tmp].keys():
if len(forward_block_dict[chrom_tmp][i]) >= 2:
line_list = block_compare(forward_block_dict[chrom_tmp][
i], reverse_block_dict[chrom_tmp], phred)
dedup_dict.update(line_list[1])
save_dict.update(line_list[0])
else:
save_dict[forward_block_dict[chrom_tmp][i][0][0]] = True
forward_block_dict[chrom_tmp].clear()
for i in reverse_block_dict[chrom_tmp].keys():
if i not in dedup_dict:
save_dict[reverse_block_dict[chrom_tmp][i][0]] = True
reverse_block_dict[chrom_tmp].clear()
save_dict.update(other_dict)
f.close()
f = pysam.AlignmentFile(in_file, "rb")
f_w = pysam.AlignmentFile(out_file, "wb", template=f)
print "total=", total, "---after dedup---", len(save_dict.keys())
total = 0
for frag in f:
if total in save_dict:
f_w.write(frag)
total += 1
f_w.close()
print "total=", total, "---after dedup---", len(save_dict.keys())
if __name__ == "__main__":
(options, args) = parseCommand()
if options.input1 == None:
print "see -h for help"
sys.exit(-1)
if options.output == None:
print "see -h for help"
sys.exit(-1)
time1 = time.time()
dedup3(options.input1, options.phred, options.output)
time2 = time.time()
print 'Time used: ' + str(time2 - time1)