Created
March 12, 2016 17:12
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import json | |
import requests, sys | |
gene_id = "ENSG00000139618" | |
gene_name = "NCOR2" | |
species = "homo_sapiens" | |
transcript = "ENSP00000384018" | |
response_isoform = requests.get("http://rest.ensembl.org/lookup/id/{}?content-type=application/json;expand=2".format(gene_id)) | |
json_data_isoform = response_isoform.content.decode("utf-8") | |
data_isoform = json.loads(json_data_isoform) | |
response_paralog = requests.get("http://rest.ensembl.org/homology/id/{}?content-type=application/json".format(gene_id)) | |
json_data_paralog = response_paralog.content.decode("utf-8") | |
data_paralog = json.loads(json_data_paralog) | |
response_motif = requests.get("http://rest.ensembl.org/overlap/translation/ENSP00000384018?content-type=application/json;type=Prosite_profiles") | |
json_data_motif = response_motif.content.decode("utf-8") | |
data_motif = json.loads(json_data_motif) | |
from collections import Counter | |
cou_isoform = Counter([transcript["biotype"] for transcript in data_isoform["Transcript"]]) | |
isoforms = cou_isoform["protein_coding"] | |
print "Number of isoforms:", isoforms | |
cou_paralog = Counter([homo["type"] for homo in data_paralog["data"][0]["homologies"]]) | |
paralogs = cou_paralog["within_species_paralog"] + 1 | |
print "Number of paralogues:", paralogs | |
cou_motif = len(data_motif) | |
print "Number of motifs:", cou_motif | |
gene_complexity = (isoforms + cou_motif) + paralogs | |
print "Complexity number:", gene_complexity |
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