def motifScan(fastafile, matrixfile, gfffile):
"""Search for motifs with existing matrix defintion"""
ive = Inclusive()
ive.fastafilename = fastafile
ive.immfilename = matrixfile
gff = ive.getMotifGff()
copy(gff, gfffile)
def kims(options):
"""Run the MotifSampler Program"""
ive = Inclusive()
ive.fastafilename = options.positives
ive.settings.setMotifLength(options.motif_length)
ive.settings.setNofMotifs(options.nof_motifs)
pgff = ive.getMotifGff()
copy(pgff, options.pgff)
#second round, find motifs in negative sequences
ive.fastafilename = options.negatives
ngff = ive.getMotifGff()
copy(ngff, options.ngff)
imm = ive.getMatrixFile()
copy(imm, options.imm)