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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='kwip_postprocess', conflict_handler='resolve',
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7 description="Postprocess galaxy kWIP 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="kWIP galaxy OUTPUT")
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11
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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
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20 with open(args.input[0]) as kwip_output:
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21 with open('kwip_postprocess_output.txt', 'w') as output:
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22 for line in kwip_output:
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23 new_line = re.sub('(_1.fastq(.gz)*|_2.fastq(.gz)*|.fastq(.gz)*)', '', line)
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24 output.write(new_line)
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25
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