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1 import itertools
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2 from sys import argv, exit
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3 from itertools import zip_longest
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4
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5 def grouper(iterable, n, fillvalue=None):
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6 args = [iter(iterable)] * n
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7 return zip_longest(*args, fillvalue=fillvalue)
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8
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9
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10 chunk_size=4
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11
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12
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13 def trimandpaste(pathToFastaFile, output):
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14 #filename = pathToFastaFile.split('/')[-1]
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15 output = open(output,"w")
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16 with open(pathToFastaFile) as f:
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17 for lines in grouper(f, chunk_size, ""): #for every chunk_sized chunk
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18 header = lines[0]
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19 seq = lines[1]
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20 sep = lines[2]
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21 qual = lines[3]
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22 trimmed_seq = seq[2:-11]+seq[-6:-1]+"\n" # fooprint + barcode
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23 UMI = seq[0:2]+seq[-11:-6] #7nt in total
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24 split_header = header.split(" ")
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25 new_header = split_header[0]+"_"+UMI+" "+split_header[1]
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26 if qual[-1:] == "\n":
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27 new_qual = qual[2:-11]+qual[-6:-1]+"\n"
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28 else:
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29 new_qual = qual[2:-10]+qual[-6:-1]
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30 output.write(new_header)
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31 output.write(trimmed_seq)
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32 output.write(sep)
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33 output.write(new_qual)
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34
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35 output.close()
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36
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37 def main():
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38 if len(argv) != 3:
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39 exit("Usage: 2 arguments required\n1: Path to fasta file \n2: name of output file")
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40
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41 # Get paths
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42 pathToFastaFile = argv[1]
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43 output = argv[2]
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44
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45 trimandpaste(pathToFastaFile, output)
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46
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47 if __name__ == "__main__":
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48 main()
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