comparison UMI_riboseq_processing/UMI.py @ 8:701804f5ad4b draft

Uploaded

7:be394fb47250

from mimetypes import guess_type
from functools import partial
from sys import argv, exit
import itertools
from itertools import zip_longest


def grouper(iterable, n, fillvalue=None):
    args = [iter(iterable)] * n
    return zip_longest(*args, fillvalue=fillvalue)


chunk_size=4

def copy_UMI_to_header_and_output_trimmed_read(pathToFastaFile, output):
    # find wheather its plain or gzipped fastq
    encoding = guess_type(pathToFastaFile)[1]  # uses file extension
    _open = partial(gzip.open, mode='rt') if encoding == 'gzip' else open
    # output file will be in gz format
    output = gzip.open(output,"wt")
    # open and parse
    with _open(pathToFastaFile) as f:
        for lines in grouper(f, chunk_size, ""):
            #lines = record.format('fastq').split('\n') # list of each record: id, seq, '+', quality
            header = lines[0]
            seq = lines[1]
            sep = lines[2]
            qual = lines[3]
            # check if  header is OK 
            if (header.startswith('@')):
                trimmed_seq = seq[2:-6]+"\n" # fooprint + barcode
                UMI = seq[0:2]+seq.rstrip()[-5:] #7nt in total; 5'NN and last 3'NNNNN
                split_header = header.split(" ")
                print (split_header)
                new_header = split_header[0]+"_"+UMI+" "+split_header[1]
                if qual[-1:] == "\n":
                    new_qual = qual[2:-6]+"\n"
                else:
                    new_qual = qual[2:-6]
                output.write(new_header)
                output.write(trimmed_seq)
                output.write(sep)
                output.write(new_qual)

    output.close()

    
def main():
    if len(argv) != 3:
        exit("Usage: 2 arguments required\n1: Path to fasta file \n2: name of output file")

    # Get paths
    pathToFastaFile = argv[1]
    output = argv[2]
    copy_UMI_to_header_and_output_trimmed_read(pathToFastaFile, output)

if __name__ == "__main__":
    main()

8:701804f5ad4b

from mimetypes import guess_type
from functools import partial
from sys import argv, exit
import itertools
from itertools import zip_longest
import subprocess
from subprocess import call

def grouper(iterable, n, fillvalue=None):
    args = [iter(iterable)] * n
    return zip_longest(*args, fillvalue=fillvalue)


def is_gz_file(filepath):
    with open(filepath, 'rb') as test_f:
        return test_f.read(2) == b'\x1f\x8b'


def lines_parse(f, output_path): 
    output = open(output_path,"w")
    for lines in grouper(f, 4, "\n"):
        header = lines[0]
        #print (header)
        seq = lines[1]
        sep = lines[2]
        qual = lines[3]
        # check if  header is OK
        if (header.startswith('@')):
            trimmed_seq = seq[2:-6]+"\n" # fooprint + barcode
            UMI = seq[0:2]+seq.rstrip()[-5:] #7nt in total; 5'NN and last 3'NNNNN
            split_header = header.split(" ")
            new_header = split_header[0]+"_"+UMI+" "+split_header[1]
            if qual[-1:] == "\n":
                new_qual = qual[2:-6]+"\n"
            else:
                new_qual = qual[2:-6]
            output.write(new_header)
            output.write(trimmed_seq)
            output.write(sep)
            output.write(new_qual)
    output.close()


def UMI_processing(pathToFastaFile, output_path):
    
    if is_gz_file(pathToFastaFile) == True: 
        with gzip.open(pathToFastaFile, 'rb') as file:
            f = [x.decode("utf-8") for x in file.readlines()]
            
    else: 
        with open(pathToFastaFile, 'r') as file:
            f = file.readlines()

    lines_parse(f, output_path)

def main():
    if len(argv) != 3:
        exit("Usage: 2 arguments required\n1: Path to fasta file \n2: name of output file")

    # Get paths
    pathToFastaFile = argv[1]
    output = argv[2]
    UMI_processing(pathToFastaFile, output)

if __name__ == "__main__":
    main()