def runMeme(infile, outfile):
'''run MEME to find motifs.
In order to increase the signal/noise ratio, MEME is not run on
all intervals but only the top 10% of intervals (peakval) are
used. Also, only the segment of 200 bp around the peak is used
and not the complete interval.
* Softmasked sequence is converted to hardmasked
sequence to avoid the detection of spurious motifs.
* Sequence is run through dustmasker
'''
PipelineMotifs.runMEMEOnSequences(infile, outfile)
def runDiscMEME(infiles, outfile):
''' Run MEME with PSP file, therefore making it
discrimenative'''
psp, fasta = infiles
PipelineMotifs.runMEMEOnSequences(fasta, outfile, psp=psp)