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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='spotyping_postprocess', conflict_handler='resolve',
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7 description="Postprocess galaxy spotyping 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('-s', '--sample', nargs='+', required=True, help="Sample names")
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11 input.add_argument('-f', '--file', nargs='+', required=True, help="File of spotyping in galaxy convention")
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12 if len(sys.argv) == 0:
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13 parser.print_usage()
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14 sys.exit(1)
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15
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16 args = parser.parse_args()
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17
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18
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19 sample_dict={}
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20
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21
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22 with open('spotyping_postprocess_output.txt', 'w') as output:
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23 index = 0
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24 for path in args.file:
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25 with open(path) as f:
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26 for line in f:
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27 #sample_dict[re.sub(".*/","",line.rstrip())] = args.sample[path_index]
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28 sample = re.sub('(_1.fastq(.gz)*|_2.fastq(.gz)*|.fastq(.gz)*)', '', args.sample[index].rstrip().lstrip())
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29 output.write(re.sub(".*.dat", sample, line))
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30 index += 1
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31
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