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1 #!/usr/bin/env python
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2
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3 # ==============================================================================
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4 # Conversion script: from MetaPhlAn output to Krona text input file
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5 # Author: Daniel Brami (daniel.brami@gmail.com)
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6 # ==============================================================================
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7
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8 import sys
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9 import optparse
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10 import re
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11
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12 def main():
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13 #Parse Command Line
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14 parser = optparse.OptionParser()
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15 parser.add_option( '-p', '--profile', dest='profile', default='', action='store', help='The input file is the MetaPhlAn standard result file' )
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16 parser.add_option( '-k', '--krona', dest='krona', default='krona.out', action='store', help='the Krona output file name' )
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17 ( options, spillover ) = parser.parse_args()
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18
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19 if not options.profile or not options.krona:
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20 parser.print_help()
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21 sys.exit()
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22
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23 re_candidates = re.compile(r"s__|unclassified\t")
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24 re_replace = re.compile(r"\w__")
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25 re_bar = re.compile(r"\|")
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26
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27 metaPhLan = list()
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28 with open(options.profile,'r') as f:
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29 metaPhLan = f.readlines()
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30 f.close()
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31
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32 krona_tmp = options.krona
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33 metaPhLan_FH = open(krona_tmp, 'w')
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34
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35 for aline in (metaPhLan):
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36 if(re.search(re_candidates, aline)):
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37 x=re.sub(re_replace, '\t', aline)
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38 x=re.sub(re_bar, '', x)
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39
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40 x_cells = x.split('\t')
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41 lineage = '\t'.join(x_cells[0:(len(x_cells) -1)])
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42 abundance = float(x_cells[-1].rstrip('\n'))
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43
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44 metaPhLan_FH.write('%s\n'%(str(abundance) + '\t' + lineage))
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45
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46 metaPhLan_FH.close()
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47
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48 if __name__ == '__main__':
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49 main()
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