Mercurial > repos > triasteran > ribogalaxy_umi_processing
comparison UMI_riboseq_processing/UMI.py @ 6:1ce4b52212c4 draft
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| author | triasteran |
|---|---|
| date | Tue, 21 Jun 2022 09:33:27 +0000 |
| parents | |
| children | be394fb47250 |
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| 5:e370df93715d | 6:1ce4b52212c4 |
|---|---|
| 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() |