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