def getGene(gid):
try:
gene = Gene.objects.filter(gene_id=gid).first()
if not gene:
baseUrl = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&rettype=fasta&id='
req = urllib2.Request(baseUrl + gid)
response = urllib2.urlopen(req)
resStr = response.read()
gene_dict = parse_fasta_str(resStr)
for gn in gene_dict.keys():
gid = gn.split('|')[1]
#get detail information
new_gene_obj = Gene(gene_id=gid)
detail_info = retrive_gene_detain(gid)
if detail_info == None:
continue
new_gene_obj.name = detail_info['name']
new_gene_obj.definition = detail_info['definition']
new_gene_obj.organism = detail_info['organism']
new_gene_obj.ntseq = gene_dict[gn]
new_gene_obj.ntseq_length = len(gene_dict[gn])
new_gene_obj.save()
return new_gene_obj
except:
traceback.print_exc()
def getGene(gid):
try:
gene = Gene.objects.filter(gene_id=gid).first()
if not gene:
baseUrl = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&rettype=fasta&id='
req = urllib2.Request(baseUrl + gid)
response = urllib2.urlopen(req)
resStr = response.read()
gene_dict = parse_fasta_str(resStr)
for gn in gene_dict.keys():
gid = gn.split('|')[1]
#get detail information
new_gene_obj = Gene(gene_id=gid)
detail_info = retrive_gene_detain(gid)
if detail_info == None:
continue
new_gene_obj.name = detail_info['name']
new_gene_obj.definition = detail_info['definition']
new_gene_obj.organism = detail_info['organism']
new_gene_obj.ntseq = gene_dict[gn]
new_gene_obj.ntseq_length = len(gene_dict[gn])
new_gene_obj.save()
return new_gene_obj
except:
traceback.print_exc()
def test_normal(self):
parse_fasta_str(self.fasta_filename)
def test_normal(self):
parse_fasta_str(self.fasta_str)
