def main(inputfile, outputfile, gfffile, gffmin, gffmax, takeStop, upstream,
downstream, verbose):
takeStart = True
if takeStop:
takeStart = False
sites = ParclipSiteContainer()
sites.loadFromFile(inputfile)
anno = gff.GFF(gfffile)
anno.filterSize(gffmin, gffmax)
anno.getChromosomePositions()
if anno.size() < 10:
print('Warning: Low number of annotation enries! ' + str(anno.size()))
fsites = ParclipSiteContainer()
percent_old = 0
percent_new = 0
for i in range(sites.size()):
if anno.isAround(sites.chrs[i], sites.pos[i], sites.strand[i],
takeStart, upstream, downstream)[1]:
fsites.addSite(sites.chrs[i], sites.pos[i], sites.m[i], sites.r[i],
sites.result[i], sites.strand[i], sites.occ[i])
percent_new = round(i / sites.size() * 100)
if percent_new > percent_old:
if verbose:
functions.showProgress(i, anno.size(), 'selecting sites')
percent_old = percent_new
fsites.save2File(outputfile)
def getEntries(sites, q1, q2):
i = 0
lower = functions.getQuantile(sites.occ,q1)
upper = functions.getQuantile(sites.occ,q2)
pc = ParclipSiteContainer()
count = 0
size = sites.size()
for i in range(sites.size()):
if sites.occ[i] > lower and sites.occ[i] <= upper:
count += 1
pc.addSite(sites.chrs[i], sites.pos[i], sites.m[i], sites.r[i], sites.result[i], sites.strand[i], sites.occ[i])
pc.getChromosomePositions()
return pc