def run0(method = '1d', win_len = 150, win_ofs = 25, spec_count =3):
'''
Build a list of jobs on the Broad within which
to compute zscores for every single locus in the
PVT1 region.
'''
ali_nums = day0.fetch_num_ali()
runs_per_rng = 500;
p0 = 0; p = []
while p0 + win_len < shape(ali_nums)[1]:
b0 = p0
p0 += win_ofs * runs_per_rng
b1 = p0
p.append(dict(win_len = win_len,
win_ofs = win_ofs,
baserng = (b0, b1),
run_id = 'run1d_single_{0}_{1}_{2}specs-{3}'.format(win_len,win_ofs,spec_count,b0),
spec_count = spec_count))
#for testing purposes, only run a small number!
if len(p) > 1000:
break
runid = 'run1d_{0}_{1}_{2}specs'.format(win_len,win_ofs,spec_count)
ll = run1d_launcher(p, runid)
ll.launch()
return ll
def remote_run_1d(run_id):
'''
'''
#GENERIC SETUP FOR A SINGLE BSUBBED PROCESS.
#Takes an input saved as a single dictionary.
#
p = butils.load_data(run_id, 'input')
#DO EVERYTHING TWIXT --------------------------------[HERE]
baserng = p['baserng']
win_len = p['win_len']
win_ofs = p['win_ofs']
spec_count = p['spec_count']
bases = (128693265,129266680)
a0 = day0.fetch_num_ali()
names = day0.fetch_alinames()
ref = a0[0]
ali_counts = sum(less(a0,4) * equal(a0, a0[0,:]) ,1)
names_all = [names[i] for i in argsort(ali_counts)[::-1]]
names = names_all[:spec_count]
a0 = a0[argsort(ali_counts)[::-1]][:spec_count]
ali_counts = sorted(ali_counts)[::-1][:spec_count]
locii, results = day0.run_windows(a0,ref, n_specs = spec_count,
win_len = win_len, win_ofs = win_ofs,
spec_names = names,
baserng = baserng)
out = {'locii':locii,
'results':results}
#AND ------------------------------------------------[HERE]
butils.save_data(out,
run_id,'output')