Script to get a list of all Schistosoma mansoni protein-coding genes from WormBase ParaSite

retrieve_smansoni_genelist_from_wormbase_parasite.py

# script to retrieve a list of all protein-coding Schistosoma mansoni genes from wormbase parasite
# example script taken from https://parasite.wormbase.org/rest-13/documentation/info/lookup_genome

import requests, sys

server = "https://parasite.wormbase.org"
ext = "/rest-13/lookup/genome/schistosoma_mansoni_prjea36577?biotypes=protein_coding"
# took the PRJEA from https://parasite.wormbase.org/Schistosoma_mansoni_prjea36577/Info/Index/

r = requests.get(server+ext, headers={ "Content-Type" : "application/json", "Accept" : ""})

if not r.ok:
    r.raise_for_status()
    sys.exit()

decoded = r.json()

# go through the genes and print them out one at a time:
cnt = 0
for gene in decoded:
    cnt += 1
    print(cnt," ",gene["id"])