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