@files_re( buildNormalizedBAM,
"(.*).normbam",
r"\1.macs" )
def runMACS( infile, outfile ):
to_cluster = False
track = infile[:-len("normbam")]
try:
control = pipeline_vitaminD.getControl( track ) + ".bam"
except AssertionError:
return
statement = '''
macs -t %(infile)s -c %(control)s \
--name=%(outfile)s \
--format=bam --tsize=35 --bw=110 --mfold=8 --gsize=6000000 >& %(outfile)s'''
P.run( **dict( locals().items() + PARAMS.items() ) )
@follows( remapWithBowtie, buildBigwig, runMACS )
def full():
pass
if __name__== "__main__":
P.checkFiles( ("genome.fasta", "genome.idx" ) )
P.checkExecutables( ("liftOver",) )
sys.exit( P.main(sys.argv) )
