gene_api.py

gene_api = """

API Rules
    - Every code block that calls to the mygene api must start with these two lines:
        import mygene
        mg = mygene.MyGeneInfo()
    - Every code block must end by assigning the output to a variable called 'ret'

API Examples

Here is an example showing how to find genes that are associated with diabetes and then find more information on those genes.

The size parameter controls how many genes you will get back.
The from_ parameter controls where in the results to start selecting from.
The query parameter controls what is being searched for

===

import mygene
mg = mygene.MyGeneInfo()

query_term="diabetes"
fields="symbol,name,entrezgene,ensemblgene"
species="human"
size=10
from_=0

gene_results = mg.query(query_term, fields=fields, species=species, size=size, from_=from_)
hits = gene_results['hits']

gene_info_list = []

for gene in hits:
    gene_info = mg.getgene(gene['_id'], fields=['name','symbol','type_of_gene','generif','genomic_pos_hg19','refseq','taxid', 'pathway'])
    gene_info_list.append(gene_info)

ret = gene_info_list

===

""".strip()