@active_if("metavelvet" in ASSEMBLERS)
@follows(buildAssemblyBowtieIndices, runMetavelvet)
@transform(SEQUENCEFILES, SEQUENCEFILES_REGEX, r"metavelvet.dir/\1.bam")
def mapReadsWithBowtieAgainstMetavelvetContigs(infile, outfile):
    PARAMS["bowtie_index_dir"] = "metavelvet.dir"
    PARAMS["genome"] = TRACKS.getTracks(infile)[0].split(".")[0]
        
    infile, reffile = infile,  os.path.join("metavelvet.dir", TRACKS.getTracks(infile)[0])
    m = PipelineMapping.Bowtie( executable = P.substituteParameters( **locals() )["bowtie_executable"] )
    statement = m.build( (infile,), outfile ) 
    P.run()

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map reads against contigs with bowtie
dataset/ETHPy150Open CGATOxford/cgat/obsolete/pipeline_genomeassembly.py/mapReadsWithBowtieAgainstMetavelvetContigs