

@follows(mkdir('kegg.dir'))
@transform(PARAMS.get('kegg_tre'), regex('(\\S+)/(\\S+).tre'), add_inputs(PARAMS.get('kegg_map')), 'kegg.dir/\\2.tsv')
def buildKeggTable(infiles, outfile):
    '\n    build kegg table mapping KO identifiers to pathways. This is\n    based on the file that was downloaded with mtools (D.Huson)\n    '
    (keggtre, keggmap) = infiles
    statement = 'python %(scriptsdir)s/keggtre2table.py \n                   --kegg-tre=%(keggtre)s\n                   --map=%(keggmap)s \n                   --log=%(outfile)s.log\n                   > %(outfile)s'
    P.run()

dataset/ETHPy150Open CGATOxford/cgat/obsolete/pipeline_metagenomecommunities.py buildKeggTable/original