def preprocess(cell_names, prefix=''):
cell_names_processed = {}
for id, entity in cell_names.items():
name, synonyms = entity
print('name::', name, "id:", id, "prefix:", prefix)
variants = []
variants.append(_cleanup(neuroner.annotate(prefix + name).annotations)) # name
for s in synonyms:
print(' syn::', s)
variants.append(_cleanup(neuroner.annotate(prefix + s).annotations)) # synonyms
cell_names_processed[id] = variants
return cell_names_processed
def test_cleanup(self):
s = Sherlok('neuroner')
an = s.annotate('layer 4 pyramidal long large neuron').annotations
clean = _cleanup(an)
self.assertEqual(clean, ['HBP_LAYER:0000004', u'HBP_MORPHOLOGY:0000001', 'Missing:long', 'Size:large'])
#print('{} ({})'.format(hbp_cell_names[hbp_id][0], hbp_id))
already_printed = []
for nlex_id, score, explain in hits_sorted[:5]:
# only if more than Neocortex
explain_str = ' '.join(flatten(explain))
if nlex_id not in already_printed and explain_str != 'ABA_REGION:315 exact same brain region':
already_printed.append(nlex_id)
#print explain_str
#print '* {} ({}, {})'.format(nlex_cell_names[nlex_id][0], round(score, 2), nlex_id)
outf.write('{}\t{}\t{}\t{}\t{}\t{}\n'.format(hbp_cell_names[hbp_id][0], hbp_id, nlex_cell_names[nlex_id][0], round(score, 2), nlex_id, explain_str))
# In[45]:
cell_= 'Nest Basket Cell' #'nest basket cell'
_cleanup(neuroner.annotate(cell_).annotations)
# In[47]:
sorted(hbp_hits['HBP_CELL:0000061'], key=get_key, reverse=True)[:5]
# In[ ]:
def test_cleanup(self):
s = Sherlok("neuroner")
an = s.annotate("layer 4 pyramidal long large neuron").annotations
clean = _cleanup(an)
self.assertEqual(clean, ["HBP_LAYER:0000004", u"HBP_MORPHOLOGY:0000001", "Missing:long", "Size:large"])