def find_orth_gene(gene, organism, target):
"""Find orthogonal gene via Gprofiler
returns a list of gene(s)"""
import pandas as pd
from gprofiler import GProfiler
gp = GProfiler()
if organism == target: # do not search if original gene is known
genes = list(set([
gene,
]))
else:
results = pd.DataFrame(
gp.orth(query=gene, organism=organism, target=target))
results.dropna(subset=["name"], axis=0)
genes = [gene for gene in results.name if gene != "N/A"]
return genes
pd.DataFrame(x['result'])
gp.convert(organism='mmusculus', query=genes )
gp.convert?
gp.convert?
gp.convert(organism='mmusculus', query=genes , target_namespace='Ensembl')
gp.convert(organism='mmusculus', query=genes , target_namespace='RefSeq')
gp.convert(organism='mmusculus', query=genes , target_namespace='UCSC')
gp.convert(organism='mmusculus', query=genes , target_namespace='Uniprot')
gp.convert(organism='mmusculus', query=genes , target_namespace='HUGO')
gp.convert(organism='mmusculus', query=genes , target_namespace='IPI')
gp.convert(organism='mmusculus', query=genes , target_namespace='ENSG')
r = requests.post(
url='https://biit.cs.ut.ee/gprofiler/api/convert/convert/',
json={
'organism':'mmusculus',
'target':'ENSG',
'query':genes,
}
)
x = r.json()
pd.DataFrame(x['result'])
gp.snpense(query=genes)
gp.snpense(query=['rs11734132', 'rs7961894', 'rs4305276', 'rs17396340'])
gp.orth(organism='mmusculus', query=genes, target='chicken')
gp.orth(organism='mmusculus', query=genes, target='human')
gp.orth(organism='mmusculus', query=genes, target='msapiens')
gp.orth(organism='mmusculus', query=genes, target='hsapiens')
gp.orth(organism='mmusculus', query=genes, target='hsapiens')
ls
%history -f pynotes_gprofiler.py
