|
5
|
1 import gzip
|
|
|
2 from mimetypes import guess_type
|
|
|
3 from functools import partial
|
|
|
4 from sys import argv, exit
|
|
|
5 import itertools
|
|
|
6 from itertools import zip_longest
|
|
|
7
|
|
|
8
|
|
|
9 def grouper(iterable, n, fillvalue=None):
|
|
|
10 args = [iter(iterable)] * n
|
|
|
11 return zip_longest(*args, fillvalue=fillvalue)
|
|
|
12
|
|
|
13
|
|
|
14 chunk_size=4
|
|
|
15
|
|
|
16 def copy_UMI_to_header_and_output_trimmed_read(pathToFastaFile, output):
|
|
|
17 # find wheather its plain or gzipped fastq
|
|
|
18 encoding = guess_type(pathToFastaFile)[1] # uses file extension
|
|
|
19 _open = partial(gzip.open, mode='rt') if encoding == 'gzip' else open
|
|
|
20 # output file will be in gz format
|
|
|
21 output = gzip.open(output,"wt")
|
|
|
22 # open and parse
|
|
|
23 with _open(pathToFastaFile) as f:
|
|
|
24 for lines in grouper(f, chunk_size, ""):
|
|
|
25 #lines = record.format('fastq').split('\n') # list of each record: id, seq, '+', quality
|
|
|
26 header = lines[0]
|
|
|
27 seq = lines[1]
|
|
|
28 sep = lines[2]
|
|
|
29 qual = lines[3]
|
|
|
30 trimmed_seq = seq[2:-6]+"\n" # fooprint + barcode
|
|
|
31 UMI = seq[0:2]+seq.rstrip()[-5:] #7nt in total; 5'NN and last 3'NNNNN
|
|
|
32 split_header = header.split(" ")
|
|
|
33 new_header = split_header[0]+"_"+UMI+" "+split_header[1]
|
|
|
34 if qual[-1:] == "\n":
|
|
|
35 new_qual = qual[2:-6]+"\n"
|
|
|
36 else:
|
|
|
37 new_qual = qual[2:-6]
|
|
|
38 output.write(new_header)
|
|
|
39 output.write(trimmed_seq)
|
|
|
40 output.write(sep)
|
|
|
41 output.write(new_qual)
|
|
|
42
|
|
|
43 output.close()
|
|
|
44
|
|
|
45
|
|
|
46 def main():
|
|
|
47 if len(argv) != 3:
|
|
|
48 exit("Usage: 2 arguments required\n1: Path to fasta file \n2: name of output file")
|
|
|
49
|
|
|
50 # Get paths
|
|
|
51 pathToFastaFile = argv[1]
|
|
|
52 output = argv[2]
|
|
|
53 copy_UMI_to_header_and_output_trimmed_read(pathToFastaFile, output)
|
|
|
54
|
|
|
55 if __name__ == "__main__":
|
|
|
56 main()
|
