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1 #!/usr/bin/env python
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2
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3 """
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4 Input: Glimmer3 prediction
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5 Output: GFF3 file
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6 Return a GFF3 file with the genes predicted by Glimmer3
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7 Bjoern Gruening
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8
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9 Note: Its not a full-fledged GFF3 file, its a really simple one.
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10
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11 """
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12
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13 import sys, re
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14
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15 def __main__():
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16 input_file = open(sys.argv[1], 'r')
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17
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18 print '##gff-version 3\n'
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19 for line in input_file:
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20 line = line.strip()
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21 if line[0] == '>':
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22 header = line[1:]
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23 else:
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24 (id, start, end, frame, score) = re.split('\s+', line)
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25 if int(end) > int(start):
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26 strand = '+'
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27 else:
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28 strand = '-'
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29 (start, end) = (end, start)
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30
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31 rest = 'frame=%s;score=%s' % (frame, score)
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32 print '\t'.join([header, 'glimmer_prediction', 'predicted_gene', start, end, '.', strand, '.', rest])
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33
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34
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35 if __name__ == "__main__" :
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36 __main__()
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