Exemplo n.º 1
0
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
Exemplo n.º 2
0
 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'])
Exemplo n.º 3
0
            #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[ ]:



Exemplo n.º 4
0
 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"])