

@transform(runBlastOnRawSequences, suffix('.blast.gz'), '.lca.gz')
def runLCA(infile, outfile):
    '\n    run the lowest common ancestor algorithm\n    on the blast output to assign reads to\n    taxa - from mtools. Runs with defaults at\n    the moment. At this point we also build\n    the functional profile using KEGG - this \n    comes with mtools package\n    '
    track = P.snip(outfile, '.lca.gz')
    outf_tax = P.snip(outfile, '.gz')
    outf_kegg = (P.snip(outf_kegg, '.lca.gz') + '.kegg.gz')
    statement = 'lcamapper.sh \n                   -k\n                   -i %(infile)s\n                   -o %(outf_tax)s > %(outfile)s.log\n                   ; gzip %(track)s.blast-kegg.txt\n                   ; gzip %(outf_tax)s\n                   ; mv %(track)s.blast-kegg.txt.gz %(outf_kegg)s'
    P.run()

dataset/ETHPy150Open CGATOxford/cgat/obsolete/pipeline_metagenomecommunities.py runLCA/VarMisuse@56/193 `outfile`->`outf_kegg`