

@follows(mkdir('metaphlan.dir'))
@transform(preprocessReads, regex('(\\S+)/(\\S+).fa'), 'metaphlan.dir/\\2.relab')
def buildMetaphlanRelativeAbundance(infile, outfile):
    '\n    metaphlan is a program used in metagenomics. It assigns\n    reads to clades based on specific genetic markers via \n    blastn searching\n    '
    to_cluster = True
    if (PARAMS['metaphlan_executable'] == 'bowtie2'):
        assert os.path.exists((PARAMS['metaphlan_db'] + '.1.bt2')), (('missing file %s: Are you sure you have the correct database for bowtie2?' % PARAMS['metaphlan_db']) + '.1.bt2')
        method = '--bowtie2db'
    elif (PARAMS['metaphlan_executable'] == 'blast'):
        assert os.path.exists((PARAMS['metaphlan_db'] + 'nin')), (('missing file %s: Are you sure you have the correct database for bowtie2?' % PARAMS['metaphlan_db']) + 'nin')
        method = '--blastdb'
    statement = PipelineMetagenomeAssembly.Metaphlan().build(infile, method='rel_ab')
    P.run()

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