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flash.py
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flash.py
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import os
import sys
import gzip
import collections
import numpy as np
from tqdm import tqdm
import _flash as fl
hamming = lambda x,y: sum(tuple(map(lambda a,b: 1 if a==b else 0, x, y))) / len(x)
convert_ascii = lambda x: [ord(asc) - 33 for asc in x]
def read_fastq(fastq_name):
"""Read fastq file
"""
seq_dict = collections.defaultdict(dict)
if fastq_name.split(".")[-1] == "gz":
f = gzip.open(fastq_name.replace("'","").replace("\\",""), mode="rt", encoding='utf-8')
else:
f = open(fastq_name.replace("'","").replace("\\",""))
n = 0
for line in f:
if line[0] == "@" and n % 4 == 0:
key = line[1:].rstrip()
key = key.split(" ")[0]
key = key.replace(":","_")
seq_dict[key]["key"] = line[1:].rstrip()
elif n%4 == 1:
seq_dict[key]["seq"] = line.rstrip()
elif n%4 == 2:
seq_dict[key]["option"] = line.rstrip()
elif n%4 == 3:
seq_dict[key]["quality"] = [ord(asc) - 33 for asc in line.rstrip()]
n += 1
f.close()
return seq_dict
def merge(seq1, seq2, score1, score2, min_overlap=50, max_overlap=300, allow_outies=True, min_identity=0.5, max_identity=1.0, cython=True):
#Pure python code to merge paired sequence. The execution speed is too slow, please use cythonized version fl.merge
seq1 = seq1.upper()
seq2 = seq2.upper()
reverse = 0
if len(seq1) >= len(seq2):
seq2 = seq2.translate(str.maketrans("ATGCRYKMSWBDHV","TACGYRMKWSVHDB"))[::-1]
score2 = score2[::-1]
else:
reverse = 1
seq1 = seq1.translate(str.maketrans("ATGCRYKMSWBDHV","TACGYRMKWSVHDB"))[::-1]
seq2, seq1 = seq1, seq2
if cython == False:
current_overlap = 0
current_score = None
current_identity = min_identity
current_slide = 0
for i in range(len(seq1)+len(seq2)):
slide = i
if i < len(seq2) and allow_outies == True:
overlap_length = i
subseq1 = seq1[:overlap_length]
subseq2 = seq2[-1*overlap_length:]
subscore1 = score1[:overlap_length]
subscore2 = score2[-1*overlap_length:]
elif i < len(seq1):
overlap_length = len(seq2)
subseq1 = seq1[i-len(seq2):i]
subseq2 = seq2
subscore1 = score1[i-len(seq2):i]
subscore2 = score2
else:
overlap_length = len(seq1) + len(seq2) - i
subseq1 = seq1[-1*overlap_length:]
subseq2 = seq2[:overlap_length:]
subscore1 = score1[-1*overlap_length:]
subscore2 = score2[:overlap_length]
if min_overlap <= overlap_length <= max_overlap:
identity = hamming(subseq1, subseq2)
if identity > current_identity or (identity == current_identity and current_overlap == 0):
current_slide = slide
current_identity = identity
current_overlap = overlap_length
current_subseq1 = subseq1
current_subseq2 = subseq2
current_subscore1 = subscore1
current_subscore2 = subscore2
#for n1, n2, s1, s2 in zip(subseq1, subseq2, subscore1, subscore2):
elif identity == current_identity:
n = 0
cscore_avg = 0
for cn1, cn2, cs1, cs2 in zip(current_subseq1, current_subseq2, current_subscore1, current_subscore2):
if cn1 != cn2:
cscore_avg += max(cs1, cs2)
n += 1
csocre_avg = cscore_avg / n
n = 0
score_avg = 0
for n1, n2, s1, s2 in zip(subseq1, subseq2, subscore1, subscore2):
if n1 != n2:
score_sum += max(s1, s2)
n += 1
score_avg = score_avg / n
if score_avg > cscore_avg:
current_slide = slide
current_identity = identity
current_overlap = overlap_length
current_subseq1 = subseq1
current_subseq2 = subseq2
current_subscore1 = subscore1
current_subscore2 = subscore2
else:
pass
if identity >= max_identity:
break
if current_identity < min_identity:
return False
else:
overlap_seq = ""
overlap_score = []
for cn1, cn2, cs1, cs2 in zip(current_subseq1, current_subseq2, current_subscore1, current_subscore2):
if cs1 > cs2:
overlap_seq += cn1
overlap_score.append(cs1)
else:
overlap_seq += cn2
overlap_score.append(cs2)
if current_slide < len(seq2) and allow_outies == True:
left_seq = seq2[:-1*overlap_length]
right_seq = seq1[overlap_length:]
left_score = score2[:-1*overlap_length]
right_score = score1[overlap_length:]
else:
left_seq = seq1[:-1*overlap_length]
right_seq = seq2[overlap_length:]
left_score = score1[:-1*overlap_length]
right_score = score2[overlap_length:]
merged_seq = left_seq + overlap_seq + right_seq
merged_score = left_score + overlap_score + right_score
else:
merged_seq, merged_score, current_slide, current_overlap, current_identity = fl.merge(seq1.encode('utf-8'), seq2.encode('utf-8'), score1, score2, min_overlap, max_overlap, allow_outies, min_identity, max_identity)
return merged_seq, merged_score, current_slide, current_overlap, current_identity
def flash(read1, read2, min_overlap=10, max_overlap=300, allow_outies=True, min_identity=0.5, max_identity=1.0, show_progress=True, key_check=True):
r1_dict = read_fastq(read1)
r2_dict = read_fastq(read2)
dist_dict = collections.defaultdict(lambda:[0, 0])
merged_dict = collections.defaultdict(dict)
if show_progress == True:
if key_check == True:
keys = [key for key in r1_dict.keys() if key in r2_dict]
keys = tqdm(keys)
else:
keys = tqdm(r1_dict.keys(), total=len(r1_dict))
else:
if key_check == True:
keys = [key for key in r1_dict.keys() if key in r2_dict]
else:
keys = r1_dict.keys()
for key in keys:
seq1 = r1_dict[key]["seq"]
seq2 = r2_dict[key]["seq"]
score1 = r1_dict[key]["quality"]
score2 = r2_dict[key]["quality"]
result = merge(seq1, seq2, score1, score2, min_overlap, max_overlap, allow_outies, min_identity, max_identity)
if result != False:
merged_dict[key]["seq"] = "".join(map(chr, result[0]))
merged_dict[key]["quality"] = result[1]
merged_dict[key]["r1_key"] = r1_dict[key]["key"]
merged_dict[key]["r2_key"] = r2_dict[key]["key"]
merged_dict[key]["identity"] = result[4]
if result[2] == 1:
dist_dict["outie", result[3]][0] += 1
dist_dict["outie", result[3]][1] += result[4]
else:
dist_dict["innie", result[3]][0] += 1
dist_dict["innie", result[3]][1] += result[4]
for key in dist_dict:
dist_dict[key][1] = dist_dict[key][1] / dist_dict[key][0]
return merged_dict, dist_dict
if __name__ == "__main__":
#path = "../../sample_data/Target-ACE_sequence_data/Rep1/AID/polyC/chr19_8211972/" #R1.fastq, R2.fastq
merged_dict, dist_dict = flash("R1.fastq.gz", "R2.fastq.gz")
for key in dist_dict:
print(key, *dist_dict[key], sep="\t")
n = 0
for key in merged_dict:
print(key, merged_dict[key]["seq"], sep="\t")
n += 1
if n == 10:
break