def mapped_reads_from_chip_ps_np(ps,mean_frag_length,cells=10000):
G = len(ps)
genome = np.zeros(G)
lamb = 1.0/mean_frag_length
for cell in (xrange(cells)):
print cell
config = rfd_xs_np(ps)
config_len = len(config)
idx = 0
l = 0
r = 0
while l < G and idx < config_len:
#print l,r,idx,config[idx]
l,r = r,r+nprand.geometric(lamb)
if l <= config[idx] < r:
#print "got hit"
genome[l:r] += 1
while idx < config_len and config[idx] < r:
idx += 1
return genome
def chip_ps_np(ps,mean_frag_length,cells=10000,verbose=False):
"""Do a chip seq experiment given the distribution ps"""
w = 10
G = len(ps)# + w - 1 #XXX HACK
cell_iterator = verbose_gen(xrange(cells),modulus=1000) if verbose else xrange(cells)
return concat(chip(G,rfd_xs_np(ps),mean_frag_length) for cell in cell_iterator)