compara-deep-learning/access_data_rest.py

import json
import requests
import progressbar
import sys

def update_protein(gene_seq,gene):
    t=0
    while(t!=2):
        try:
            server = "https://rest.ensembl.org"
            ext = "/sequence/id/"+str(gene)+"?type=protein;multiple_sequences=1"

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

            if not r.ok:
                r.raise_for_status()
                sys.exit()
            r=r.json()
            if len(r)==1:
                r=dict(r[0])
                gene_seq[gene]=str(r["seq"])
                return
            else:
                maxi=0
                maxlen=0
                for i in range(len(r)):
                    m=r[i]
                    m=dict(m)
                    if len(m["seq"])>maxlen:
                        maxi=i
                r=dict(r[maxi])
                gene_seq[gene]=str(r["seq"])
                return
        except :
            t+=1
            #print("\nError:",e)
            continue
    gene_seq[gene]=""

def update_rest_protein(data):
    gids={}
    with open("processed/not_found.json","r") as file:
        gids=dict(json.load(file))

    gids=list(gids.keys())

    geneseq={}

    server = "https://rest.ensembl.org"
    ext = "/sequence/id?type=protein"
    headers={ "Content-Type" : "application/json", "Accept" : "application/json"}

    for i in progressbar.progressbar(range(0,len(gids)-50,50)):
        ids=dict(ids=list(gids[i:i+50]))
        while(1):
            try:
                r = requests.post(server+ext, headers=headers, data=str(json.dumps(ids)))
                if not r.ok:
                    r.raise_for_status()
                gs=r.json()
                tgs={}
                for g in gs:
                    tgs[g["query"]]=g["seq"]
                geneseq.update(tgs)
                break
            except Exception as e:
                print("Error:",e)
                continue

    data.update(geneseq)
    for genes in gids:
        try:
            _=data[genes]
        except:
            print(genes)
            update_protein(data,genes)

    print("Gene Sequences Updated Successfully")
    return data
            
def update(gene_seq,gene):
    t=0
    while(t!=2):
        try:
            server = "https://rest.ensembl.org"
            ext = "/sequence/id/"+str(gene)+"?type=cds;multiple_sequences=1"

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

            if not r.ok:
                r.raise_for_status()
                sys.exit()
            r=r.json()
            if len(r)==1:
                r=dict(r[0])
                gene_seq[gene]=str(r["seq"])
                return
            else:
                maxi=0
                maxlen=0
                for i in range(len(r)):
                    m=r[i]
                    m=dict(m)
                    if len(m["seq"])>maxlen:
                        maxi=i
                r=dict(r[maxi])
                gene_seq[gene]=str(r["seq"])
                return
        except Exception as e:
            t+=1
            #print("\nError:",e)
            continue
    gene_seq[gene]=""

def update_rest(data,fname):
    gids={}
    with open("processed/not_found_"+fname+".json","r") as file:
        gids=dict(json.load(file))

    gids=list(gids.keys())

    geneseq={}

    server = "https://rest.ensembl.org"
    ext = "/sequence/id?type=cds"
    headers={ "Content-Type" : "application/json", "Accept" : "application/json"}

    for i in progressbar.progressbar(range(0,len(gids)-50,50)):
        ids=dict(ids=list(gids[i:i+50]))
        while(1):
            try:
                r = requests.post(server+ext, headers=headers, data=str(json.dumps(ids)))
                if not r.ok:
                    r.raise_for_status()
                gs=r.json()
                tgs={}
                for g in gs:
                    tgs[g["query"]]=g["seq"]
                geneseq.update(tgs)
                break
            except Exception as e:
                print("Error:",e)
                continue

    data.update(geneseq)
    for genes in gids:
        try:
            _=data[genes]
        except:
            print(genes)
            update(data,genes)

    print("Gene Sequences Updated Successfully")
    return data