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1 #!/usr/bin/env python
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2
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3 from __future__ import with_statement
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4
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5 import sys
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6 import os
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7 import argparse
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8
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9 def read_params(args):
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10 parser = argparse.ArgumentParser(description='Convert LEfSe output to '
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11 'Circlader input')
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12 parser.add_argument( 'inp_f', metavar='INPUT_FILE', nargs='?',
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13 default=None, type=str,
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14 help="the input file [stdin if not present]")
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15 parser.add_argument( 'out_f', metavar='OUTPUT_FILE', nargs='?',
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16 default=None, type=str,
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17 help="the output file [stdout if not present]")
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18 parser.add_argument('-l', metavar='levels with label', default=0, type=int)
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19
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20 return vars(parser.parse_args())
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21
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22 def lefse2circlader(par):
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23 finp,fout = bool(par['inp_f']), bool(par['out_f'])
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24
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25 with open(par['inp_f']) if finp else sys.stdin as inpf:
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26 put_bm = (l.strip().split('\t') for l in inpf.readlines())
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27 biomarkers = [p for p in put_bm if len(p) > 2]
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28
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29 circ = [ [ b[0],
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30 "" if b[0].count('.') > par['l'] else b[0].split('.')[-1],
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31 b[2],
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32 b[2]+"_col" ] for b in biomarkers]
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33
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34 with open(par['out_f'],'w') if fout else sys.stdout as out_file:
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35 for c in circ:
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36 out_file.write( "\t".join( c ) + "\n" )
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37
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38 if __name__ == '__main__':
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39 params = read_params(sys.argv)
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40 lefse2circlader(params)
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41
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