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4
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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 Bio import SeqIO
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0
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5 from sys import argv, exit
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6
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4
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7 def copy_UMI_to_header_and_output_trimmed_read(pathToFastaFile, output):
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8 # find wheather its plain or gzipped fastq
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9 encoding = guess_type(pathToFastaFile)[1] # uses file extension
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10 _open = partial(gzip.open, mode='rt') if encoding == 'gzip' else open
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11 # output file will be in gz format
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12 output = gzip.open(output,"wt")
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13 # open and parse
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14 with _open(pathToFastaFile) as f:
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15 for record in SeqIO.parse(f, 'fastq'):
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16 lines = record.format('fastq').split('\n') # list of each record: id, seq, '+', quality
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0
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17 header = lines[0]
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18 seq = lines[1]
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19 sep = lines[2]
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20 qual = lines[3]
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3
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21 trimmed_seq = seq[2:-6]+"\n" # fooprint + barcode
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4
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22 UMI = seq[0:2]+seq.rstrip()[-5:] #7nt in total; 5'NN and last 3'NNNNN
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0
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23 split_header = header.split(" ")
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24 new_header = split_header[0]+"_"+UMI+" "+split_header[1]
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25 if qual[-1:] == "\n":
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3
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26 new_qual = qual[2:-6]+"\n"
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0
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27 else:
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3
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28 new_qual = qual[2:-6]
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4
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29 output.write(new_header+'\n')
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30 output.write(trimmed_seq)
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31 output.write(sep+'\n')
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32 output.write(new_qual+'\n')
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0
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33
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4
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34 output.close()
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0
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35
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36 def main():
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4
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37 if len(argv) != 3:
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0
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38 exit("Usage: 2 arguments required\n1: Path to fasta file \n2: name of output file")
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39
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40 # Get paths
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41 pathToFastaFile = argv[1]
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42 output = argv[2]
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4
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43 copy_UMI_to_header_and_output_trimmed_read(pathToFastaFile, output)
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0
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44
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45 if __name__ == "__main__":
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46 main()
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