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4
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1 #!/usr/bin/env python
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2
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3 import sys
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4 import argparse as ap
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5 import re
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6 parser = ap.ArgumentParser(prog='prince_postprocess', conflict_handler='resolve',
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7 description="Postprocess galaxy PRINCE output")
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8
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9 input = parser.add_argument_group('Input', '')
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10 input.add_argument('-i', '--input', nargs=1, required=True, help="PRINCE OUTPUT")
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8
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11 input.add_argument('-s', '--sample', nargs='+', required=True, help="Sample names")
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12 input.add_argument('-f', '--file', nargs='+', required=True, help="File of forward reads in galaxy convention")
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4
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13 if len(sys.argv) == 0:
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14 parser.print_usage()
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15 sys.exit(1)
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16
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17 args = parser.parse_args()
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18
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19 #print(args.input)
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20 #sample_name = re.sub('(_1.fastq(.gz)*|_2.fastq(.gz)*|.fastq(.gz)*)', '', args.label.rstrip().lstrip())
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8
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21 sample_dict={}
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22 path_index = 0
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23 for path in args.file:
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24 with open(path) as f:
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25 for line in f:
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9
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26 sample_dict[re.sub(".*/","",line.rstrip())] = args.sample[path_index]
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8
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27 path_index += 1
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28
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29
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30
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31
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32
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33
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4
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34
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35 with open(args.input[0]) as prince_output:
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36 with open('prince_postprocess_output.txt', 'w') as output:
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37 x = 1
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38 index = 0
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39 for line in prince_output:
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40 if x%2 == 0:
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8
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41 entries =line.rstrip().split(',')
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42 sample = re.sub('(_1.fastq(.gz)*|_2.fastq(.gz)*|.fastq(.gz)*)', '', sample_dict[entries[0]])
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43 output.write(re.sub(entries[0], sample, line))
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4
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44 index += 1
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45 else:
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46 output.write(line)
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47 x += 1
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48 #output.write("\n")
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49
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50
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