hmm.pssm.ModelBuilder(order).dump_background_mosaic_model(hmm.as_state_model(model), self.path_for(index))
_global_cache = None
def global_background_model_cache():
global _global_cache
if None == _global_cache:
_global_cache = BackgroundModelCache()
return _global_cache
def background_model(order, N):
return hmm.as_state_model(global_background_model_cache().load((order, N, 'T00594')))
if '__main__' == __name__:
try:
import cookbook
cookbook.make_current_process_nice()
except:
print 'Could not set process priority'
def bw_callback(LL): pass; #print 'LL: %.3f' % LL
order = 0
num_mosaics = 1
cache = BackgroundModelCache()
print ' fragment order # mosaics LL/base'
for fragment in all_fragments:
seqs = seqs_for_fragment(fragment)
model_builder = hmm.pssm.ModelBuilder(order)
training_sequences = [ model_builder.converter.to_order_n(s) for s in seqs ]
known_bases = sum(model_builder.converter.num_known_bases_order_n(s) for s in training_sequences)
