Mercurial > repos > triasteran > ribogalaxy_umi_processing

comparison UMI_riboseq_tool/UMI.py @ 10:d003917eaf2c draft

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author jackcurragh
date Fri, 15 Jul 2022 12:43:45 +0000
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children 0b5c3e35cddb
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9:31438c26afec 10:d003917eaf2c
1 import gzip
2 from sys import argv, exit
3 from itertools import zip_longest
4 from Bio import SeqIO
5
6 def grouper(iterable, n, fillvalue=None):
7 args = [iter(iterable)] * n
8 return zip_longest(*args, fillvalue=fillvalue)
9
10
11 def is_gz_file(filepath):
12 with open(filepath, 'rb') as test_f:
13 return test_f.read(2) == b'\x1f\x8b'
14
15
16 def process_fastq_record(record, output, UMI_5_prime_length=2, UMI_3_prime_length=5):
17 '''
18 Write UMI to FASTQ header for given biopython record to given open output
19 UMI_5_prime_length number of bases to trim from 5' and write to header
20 UMI_3_prime_length number of bases to trim from 3' and write to header
21 defaults are for McGlincy Ingolia Protocol
22 '''
23 lines = record.format('fastq').split('\n') # all 4 lines
24 header = lines[0]
25 seq = lines[1]
26 sep = lines[2]
27 qual = lines[3]
28
29 if (header.startswith('@')):
30 trimmed_seq = seq[UMI_5_prime_length:-(UMI_3_prime_length + 1)] # fooprint + barcode
31 UMI = seq[0:UMI_5_prime_length]+seq.rstrip()[-UMI_3_prime_length:len(seq)] #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 new_qual = qual[UMI_5_prime_length:-(UMI_3_prime_length + 1)]
35 output.write(new_header+'\n')
36 output.write(trimmed_seq+'\n')
37 output.write(sep+'\n')
38 output.write(new_qual+'\n')
39
40
41
42 def UMI_processing(pathToFastaFile, output_path, bool_gzip, UMI_5_prime_length, UMI_3_prime_length):
43
44 if bool_gzip:
45 output = gzip.open(output_path,"wt")
46 else:
47 output = open(output_path, 'w')
48
49 if is_gz_file(pathToFastaFile) == True:
50 print ('file is gzipped fastq')
51 with gzip.open(pathToFastaFile, "rt") as handle:
52 for i, record in enumerate(SeqIO.parse(handle, "fastq")):
53 process_fastq_record(record, output, UMI_5_prime_length=2, UMI_3_prime_length=5)
54
55 else:
56 for record in SeqIO.parse(pathToFastaFile, 'fastq'):
57 process_fastq_record(record, output, UMI_5_prime_length, UMI_3_prime_length)
58
59 output.close()
60
61
62
63
64 def main():
65 if len(argv) != 6:
66 exit("Usage: 3 arguments required\n1: Path to fasta file \n2: name of output file\n3: string 'True' or 'False' whether to gzip output")
67
68 # Get paths
69 pathToFastaFile = argv[1]
70 output = argv[2]
71 bool_gzip = True if argv[3].lower().capitalize() == 'True' else False
72 UMI_5_prime_length = argv[4]
73 UMI_3_prime_length = argv[5]
74 UMI_processing(pathToFastaFile, output, bool_gzip, UMI_5_prime_length, UMI_3_prime_length)
75
76 if __name__ == "__main__":
77 main()