

@follows(mkdir('kegg.dir'))
@transform(runLCA, regex('(\\S+)/(\\S+).lca.gz'), add_inputs(buildKeggTable), 'kegg.dir/\\2.kegg.counts')
def countKeggAssociations(infiles, outfile):
    '\n    count the number of reads associted with Kegg pathways\n    '
    infile = infiles[0].replace('.lca', '.kegg')
    kegg_table = infiles[1]
    level = PARAMS.get('kegg_level')
    statement = 'zcat %(infile)s |\n                   python %(scriptsdir)s/lcakegg2counts.py\n                   --kegg-table=%(kegg_table)s\n                   --level=%(level)s\n                   --method=proportion\n                   --log=%(outfile)s.log\n                   > %(outfile)s'
    P.run()

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