mirror of
https://github.com/Priyatham-sai-chand/compara-deep-learning.git
synced 2026-08-15 04:01:14 -07:00
Add files via upload
This commit is contained in:
HarshitGupta11
GitHub
parent
647b2c9140
commit
855c89df56
1 changed files with 79 additions and 103 deletions
|
|
@ -3,176 +3,152 @@ import requests
|
|||
import progressbar
|
||||
import sys
|
||||
|
||||
|
||||
def update_protein(gene_seq, gene):
|
||||
t = 0
|
||||
while(t != 2):
|
||||
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"
|
||||
ext = "/sequence/id/"+str(gene)+"?type=protein;multiple_sequences=1"
|
||||
|
||||
r = requests.get(
|
||||
server + ext,
|
||||
headers={
|
||||
"Content-Type": "application/json"})
|
||||
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"])
|
||||
r=r.json()
|
||||
if len(r)==1:
|
||||
r=dict(r[0])
|
||||
gene_seq[gene]=str(r["seq"])
|
||||
return
|
||||
else:
|
||||
maxi = 0
|
||||
maxlen = 0
|
||||
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"])
|
||||
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 BaseException:
|
||||
t += 1
|
||||
# print("\nError:",e)
|
||||
except :
|
||||
t+=1
|
||||
#print("\nError:",e)
|
||||
continue
|
||||
gene_seq[gene] = ""
|
||||
gene_seq[gene]=""
|
||||
|
||||
def update_rest_protein(data,fname):
|
||||
gids={}
|
||||
with open("processed/not_found_"+fname+".json","r") as file:
|
||||
gids=dict(json.load(file))
|
||||
|
||||
def update_rest_protein(data):
|
||||
gids = {}
|
||||
with open("processed/not_found.json", "r") as file:
|
||||
gids = dict(json.load(file))
|
||||
gids=list(gids.keys())
|
||||
|
||||
gids = list(gids.keys())
|
||||
|
||||
geneseq = {}
|
||||
geneseq={}
|
||||
|
||||
server = "https://rest.ensembl.org"
|
||||
ext = "/sequence/id?type=protein"
|
||||
headers = {
|
||||
"Content-Type": "application/json",
|
||||
"Accept": "application/json"}
|
||||
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]))
|
||||
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)))
|
||||
r = requests.post(server+ext, headers=headers, data=str(json.dumps(ids)))
|
||||
if not r.ok:
|
||||
r.raise_for_status()
|
||||
gs = r.json()
|
||||
tgs = {}
|
||||
gs=r.json()
|
||||
tgs={}
|
||||
for g in gs:
|
||||
tgs[g["query"]] = g["seq"]
|
||||
tgs[g["query"]]=g["seq"]
|
||||
geneseq.update(tgs)
|
||||
break
|
||||
except Exception as e:
|
||||
print("Error:", e)
|
||||
print("Error:",e)
|
||||
continue
|
||||
|
||||
data.update(geneseq)
|
||||
for genes in gids:
|
||||
try:
|
||||
_ = data[genes]
|
||||
except BaseException:
|
||||
_=data[genes]
|
||||
except:
|
||||
print(genes)
|
||||
update_protein(data, genes)
|
||||
update_protein(data,genes)
|
||||
|
||||
print("Gene Sequences Updated Successfully")
|
||||
print("Protein Sequences Updated Successfully")
|
||||
return data
|
||||
|
||||
|
||||
def update(gene_seq, gene):
|
||||
t = 0
|
||||
while(t != 2):
|
||||
|
||||
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"
|
||||
ext = "/sequence/id/"+str(gene)+"?type=cds;multiple_sequences=1"
|
||||
|
||||
r = requests.get(
|
||||
server + ext,
|
||||
headers={
|
||||
"Content-Type": "application/json"})
|
||||
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"])
|
||||
r=r.json()
|
||||
if len(r)==1:
|
||||
r=dict(r[0])
|
||||
gene_seq[gene]=str(r["seq"])
|
||||
return
|
||||
else:
|
||||
maxi = 0
|
||||
maxlen = 0
|
||||
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"])
|
||||
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 BaseException:
|
||||
t += 1
|
||||
# print("\nError:",e)
|
||||
except Exception as e:
|
||||
t+=1
|
||||
#print("\nError:",e)
|
||||
continue
|
||||
gene_seq[gene] = ""
|
||||
gene_seq[gene]=""
|
||||
|
||||
def update_rest(data,fname):
|
||||
gids={}
|
||||
with open("processed/not_found_"+fname+".json","r") as file:
|
||||
gids=dict(json.load(file))
|
||||
|
||||
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())
|
||||
|
||||
gids = list(gids.keys())
|
||||
|
||||
geneseq = {}
|
||||
geneseq={}
|
||||
|
||||
server = "https://rest.ensembl.org"
|
||||
ext = "/sequence/id?type=cds"
|
||||
headers = {
|
||||
"Content-Type": "application/json",
|
||||
"Accept": "application/json"}
|
||||
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]))
|
||||
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)))
|
||||
r = requests.post(server+ext, headers=headers, data=str(json.dumps(ids)))
|
||||
if not r.ok:
|
||||
r.raise_for_status()
|
||||
gs = r.json()
|
||||
tgs = {}
|
||||
gs=r.json()
|
||||
tgs={}
|
||||
for g in gs:
|
||||
tgs[g["query"]] = g["seq"]
|
||||
tgs[g["query"]]=g["seq"]
|
||||
geneseq.update(tgs)
|
||||
break
|
||||
except Exception as e:
|
||||
print("Error:", e)
|
||||
print("Error:",e)
|
||||
continue
|
||||
|
||||
data.update(geneseq)
|
||||
for genes in gids:
|
||||
try:
|
||||
_ = data[genes]
|
||||
except BaseException:
|
||||
_=data[genes]
|
||||
except:
|
||||
print(genes)
|
||||
update(data, genes)
|
||||
update(data,genes)
|
||||
|
||||
print("Gene Sequences Updated Successfully")
|
||||
return data
|
||||
return data
|
||||
Loading…
Reference in a new issue