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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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11 input.add_argument('-s', '--sample', nargs='*', required=True, help="Sample names")
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12
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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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21
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22 with open(args.input[0]) as prince_output:
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23 with open('prince_postprocess_output.txt', 'w') as output:
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24 x = 1
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25 index = 0
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26 for line in prince_output:
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27 if x%2 == 0:
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28 sample = re.sub('(_1.fastq(.gz)*|_2.fastq(.gz)*|.fastq(.gz)*)', '', args.sample[index])
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29 output.write(re.sub('.*.dat', sample, line))
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30 index += 1
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31 else:
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32 output.write(line)
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33 x += 1
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34 #output.write("\n")
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35
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36
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