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Added Extra Try and Catch

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HarshitGupta11 2019-06-11 13:40:15 +05:30 committed by GitHub
parent d7f6ccf87c
commit 0cb98b0ca0
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1 changed files with 25 additions and 15 deletions
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40
create_synteny_matrix.py
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@ -8,16 +8,21 @@ from skbio.alignment import local_pairwise_align_ssw
from skbio import DNA,TabularMSA,RNA
def update(gene_seq,gene):
server = "https://rest.ensembl.org"
ext = "/sequence/id/"+str(gene)+"?"
while(1):
try:
server = "https://rest.ensembl.org"
ext = "/sequence/id/"+str(gene)+"?"
r = requests.get(server+ext, headers={ "Content-Type" : "text/plain"})
r = requests.get(server+ext, headers={ "Content-Type" : "text/plain"})
if not r.ok:
r.raise_for_status()
sys.exit()
if not r.ok:
r.raise_for_status()
sys.exit()
gene_seq[gene]=str(r.text)
gene_seq[gene]=str(r.text)
return
except:
continue
def create_synteny_matrix_mul(gene_seq,g1,g2,n):
for gene in g1:
@ -46,14 +51,17 @@ def create_synteny_matrix_mul(gene_seq,g1,g2,n):
if g2[j]=="NULL_GENE":
continue
norm_len=max(len(gene_seq[g1[i]]),len(gene_seq[g2[j]]))
result = ed.align(gene_seq[g1[i]],gene_seq[g2[j]], mode="NW", task="distance")
sm[i][j][0]=result["editDistance"]/(norm_len)
result = ed.align(gene_seq[g1[i]],gene_seq[g2[j]][::-1], mode="NW", task="distance")
sm[i][j][1]=result["editDistance"]/(norm_len)
_,result,_=local_pairwise_align_ssw(DNA(gene_seq[g1[i]]),DNA(gene_seq[g2[j]]))
sml[i][j][0]=result/(norm_len)
_,result,_=local_pairwise_align_ssw(DNA(gene_seq[g1[i]]),DNA(gene_seq[g2[j]][::-1]))
sml[i][j][1]=result/(norm_len)
try:
result = ed.align(gene_seq[g1[i]],gene_seq[g2[j]], mode="NW", task="distance")
sm[i][j][0]=result["editDistance"]/(norm_len)
result = ed.align(gene_seq[g1[i]],gene_seq[g2[j]][::-1], mode="NW", task="distance")
sm[i][j][1]=result["editDistance"]/(norm_len)
_,result,_=local_pairwise_align_ssw(DNA(gene_seq[g1[i]]),DNA(gene_seq[g2[j]]))
sml[i][j][0]=result/(norm_len)
_,result,_=local_pairwise_align_ssw(DNA(gene_seq[g1[i]]),DNA(gene_seq[g2[j]][::-1]))
sml[i][j][1]=result/(norm_len)
except:
return np.zeros((n,n,2)),np.zeros((n,n,2))
return sm,sml
def synteny_matrix(gene_seq,hdf,lsy,n,enable_break):
@ -87,6 +95,8 @@ def synteny_matrix(gene_seq,hdf,lsy,n,enable_break):
assert(len(x)==len(y))
assert(len(x)==(2*n+1))
smgtemp,smltemp=create_synteny_matrix_mul(gene_seq,x,y,2*n+1)
if np.all(smgtemp==0):
continue
sg.append(smgtemp)
sl.append(smltemp)
ind.append(index)