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1 #!/usr/bin/env python3
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2 '''
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3 Purpose of this script is to filters some massages output
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4 stderr to prevent galaxy to raise the error
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5 '''
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6 import sys
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7
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8 string_to_detect = [
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9 'Karlin-Altschul parameters',
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10 'slippage may introduce errors',
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11 'Examining 5 or more matches is recommended',
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12 'DeprecationWarning: The binary mode of fromstring is deprecated',
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13 ]
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14
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15 string_to_remove = [
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16 ('error', 'errour'),
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17 ('warning', 'alert')
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18 ]
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19 input_file = sys.argv[1]
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20
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21 with open(input_file) as f:
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22 for line in f:
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23 for s in string_to_detect:
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24 if s in line:
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25 new_line = "--" + line.lower()
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26 for r in string_to_remove:
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27 new_line = new_line.replace(r[0], r[1])
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28 line = new_line
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29 print("parsed line:", line, file=sys.stderr)
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