Python get_GO Examples

Example #1

File: mirnaExample4.py Project: zidarsk8/orange-bio

import random
import obiGO
import obimiRNA

annotations = obiGO.Annotations('hsa', obiGO.Ontology())

miRNAs = random.sample(obimiRNA.ids('hsa'), 10)

dict_all = obimiRNA.get_GO(miRNAs, annotations, goSwitch=False)
dict_enr = obimiRNA.get_GO(miRNAs,
                           annotations,
                           enrichment=True,
                           goSwitch=False)

dict_tfidf = obimiRNA.filter_GO(dict_all, annotations, reverse=False)

print '#\tmiRNA name\t# All GO terms\t# Enriched GO terms\t# Filtred GO terms\n'
for n, m in enumerate(miRNAs):
    print '%d\t%s\t\t%d\t\t%d\t\t%d' % (n + 1, m, len(
        dict_all[m]), len(dict_enr[m]), len(dict_tfidf[m]))

Example #2

File: mirnaExample4.py Project: JakaKokosar/orange-bio

import random
import obiGO
import obimiRNA

annotations = obiGO.Annotations('hsa',obiGO.Ontology())

miRNAs = random.sample(obimiRNA.ids('hsa'),10)

dict_all = obimiRNA.get_GO(miRNAs, annotations, goSwitch=False)
dict_enr = obimiRNA.get_GO(miRNAs, annotations, enrichment=True, goSwitch=False)

dict_tfidf = obimiRNA.filter_GO(dict_all, annotations, reverse=False)

print '#\tmiRNA name\t# All GO terms\t# Enriched GO terms\t# Filtred GO terms\n'
for n,m in enumerate(miRNAs):
    print '%d\t%s\t\t%d\t\t%d\t\t%d' % (n+1,m,len(dict_all[m]),len(dict_enr[m]),len(dict_tfidf[m]))

Example #3

File: mirnaExample3.py Project: zidarsk8/orange-bio

import random
import obiGO
import obimiRNA

annotations = obiGO.Annotations('hsa',obiGO.Ontology())
miRNAs = random.sample(obimiRNA.ids('hsa'),10)

print 'miRNA\tNumber of annotations\tGO_IDs\n'
for mi,goList in obimiRNA.get_GO(miRNAs, annotations, goSwitch=False).items():
    if goList:
        print '%s\t%d\t%s' % (mi, len(goList), ','.join(goList[0:4])+'...')