def doProcessRender(self, request):
self.setLayout('public/blast.html')
if (request.method == "POST"):
fileDict = request.FILES
response = ""
if (request.POST.has_key('blast_db')):
database = request.POST['blast_db']
root = settings.STATIC_ROOT
media_root = settings.MEDIA_ROOT
landmark = Landmark.objects.get(organism_id__exact=int(database))
#os.system("formatdb -p F -i " + root + "/" + str(landmark.name).lower() + ".fasta")
sequence = request.POST['sequence']
if (sequence != ""):
tmp_fasta_file = NamedTemporaryFile(mode='w+b', suffix='.fasta', dir='/tmp', delete=False)
tmp_fasta_file.write(sequence)
tmp_fasta_file.close()
blast_result = os.popen("blastall -p blastn -d " + root + "/" + str(landmark.name).lower() + ".fasta -T T -i " + root + "/tmp.fasta")
response = "<pre>" + " ".join(blast_result.readlines()) + "</pre>"
os.remove(tmp_fasta_file.name)
elif (fileDict.has_key('file')):
uploadedFile = fileDict['file']
fasta = BlastUpload(fasta_file=uploadedFile, name=uploadedFile.name)
fasta.save()
blast_result = os.popen("blastall -p blastn -d " + root + "/" + str(landmark.name).lower() + ".fasta -T T -i " + media_root + "/" + str(fasta.fasta_file))
response = "<pre>" + " ".join(blast_result.readlines()) + "</pre>"
os.system("rm " + root + "/" + str(landmark.name).lower() + ".fasta.n*")
os.system("rm " + media_root + "/" + str(fasta.fasta_file))
fasta.delete()
return {
'response' : response
}
def submit_blast(request):
if (request.method == "POST"):
postDict = request.POST
fileDict = request.FILES
response = ""
if (postDict.has_key('blast_db')):
database = postDict['blast_db']
root = settings.STATIC_ROOT
media_root = settings.MEDIA_ROOT
landmark = Landmark.objects.get(organism_id__exact=int(database))
os.system("formatdb -p F -i " + root + "/" +
str(landmark.name).lower() + ".fasta")
sequence = postDict['sequence']
if (sequence != ""):
tmp_fasta_file = open(root + "/tmp.fasta", "w")
tmp_fasta_file.write(sequence)
tmp_fasta_file.close()
blast_result = os.popen("blastall -p blastn -d " + root + "/" +
str(landmark.name).lower() +
".fasta -T T -i " + root +
"/tmp.fasta")
response = "<pre>" + " ".join(
blast_result.readlines()) + "</pre>"
os.system("rm " + root + "/" + str(landmark.name).lower() +
".fasta.n*")
os.system("rm " + root + "/tmp.fasta")
elif (fileDict.has_key('file')):
uploadedFile = fileDict['file']
fasta = BlastUpload(fasta_file=uploadedFile,
name=uploadedFile.name)
fasta.save()
blast_result = os.popen("blastall -p blastn -d " + root + "/" +
str(landmark.name).lower() +
".fasta -T T -i " + media_root + "/" +
str(fasta.fasta_file))
response = "<pre>" + " ".join(
blast_result.readlines()) + "</pre>"
os.system("rm " + root + "/" + str(landmark.name).lower() +
".fasta.n*")
os.system("rm " + media_root + "/" + str(fasta.fasta_file))
fasta.delete()
#response = "blastall -p blastn -d " + root + "/" + landmark.name.lower() + ".fasta -m 0 -i " + media_root + "/" + str(fasta.fasta_file)
# change this to the results page
#return HttpResponseRedirect(reverse('mycoplasma_home.views.blast'))
return HttpResponse(response)
else:
error = "Not a Post"
return HttpResponse("Error: " + error)
def doProcessRender(self, request):
self.setLayout('public/blast.html')
if (request.method == "POST"):
fileDict = request.FILES
response = ""
if (request.POST.has_key('blast_db')):
database = request.POST['blast_db']
root = settings.STATIC_ROOT
media_root = settings.MEDIA_ROOT
landmark = Landmark.objects.get(
organism_id__exact=int(database))
#os.system("formatdb -p F -i " + root + "/" + str(landmark.name).lower() + ".fasta")
sequence = request.POST['sequence']
if (sequence != ""):
tmp_fasta_file = NamedTemporaryFile(mode='w+b',
suffix='.fasta',
dir='/tmp',
delete=False)
tmp_fasta_file.write(sequence)
tmp_fasta_file.close()
blast_result = os.popen("blastall -p blastn -d " + root +
"/" + str(landmark.name).lower() +
".fasta -T T -i " + root +
"/tmp.fasta")
response = "<pre>" + " ".join(
blast_result.readlines()) + "</pre>"
os.remove(tmp_fasta_file.name)
elif (fileDict.has_key('file')):
uploadedFile = fileDict['file']
fasta = BlastUpload(fasta_file=uploadedFile,
name=uploadedFile.name)
fasta.save()
blast_result = os.popen("blastall -p blastn -d " + root +
"/" + str(landmark.name).lower() +
".fasta -T T -i " + media_root +
"/" + str(fasta.fasta_file))
response = "<pre>" + " ".join(
blast_result.readlines()) + "</pre>"
os.system("rm " + root + "/" + str(landmark.name).lower() +
".fasta.n*")
os.system("rm " + media_root + "/" + str(fasta.fasta_file))
fasta.delete()
return {'response': response}
def submit_blast(request):
if request.method == "POST":
postDict = request.POST
fileDict = request.FILES
response = ""
if postDict.has_key("blast_db"):
database = postDict["blast_db"]
root = settings.STATIC_ROOT
media_root = settings.MEDIA_ROOT
landmark = Landmark.objects.get(organism_id__exact=int(database))
os.system("formatdb -p F -i " + root + "/" + str(landmark.name).lower() + ".fasta")
sequence = postDict["sequence"]
if sequence != "":
tmp_fasta_file = open(root + "/tmp.fasta", "w")
tmp_fasta_file.write(sequence)
tmp_fasta_file.close()
blast_result = os.popen(
"blastall -p blastn -d "
+ root
+ "/"
+ str(landmark.name).lower()
+ ".fasta -T T -i "
+ root
+ "/tmp.fasta"
)
response = "<pre>" + " ".join(blast_result.readlines()) + "</pre>"
os.system("rm " + root + "/" + str(landmark.name).lower() + ".fasta.n*")
os.system("rm " + root + "/tmp.fasta")
elif fileDict.has_key("file"):
uploadedFile = fileDict["file"]
fasta = BlastUpload(fasta_file=uploadedFile, name=uploadedFile.name)
fasta.save()
blast_result = os.popen(
"blastall -p blastn -d "
+ root
+ "/"
+ str(landmark.name).lower()
+ ".fasta -T T -i "
+ media_root
+ "/"
+ str(fasta.fasta_file)
)
response = "<pre>" + " ".join(blast_result.readlines()) + "</pre>"
os.system("rm " + root + "/" + str(landmark.name).lower() + ".fasta.n*")
os.system("rm " + media_root + "/" + str(fasta.fasta_file))
fasta.delete()
# response = "blastall -p blastn -d " + root + "/" + landmark.name.lower() + ".fasta -m 0 -i " + media_root + "/" + str(fasta.fasta_file)
# change this to the results page
# return HttpResponseRedirect(reverse('mycoplasma_home.views.blast'))
return HttpResponse(response)
else:
error = "Not a Post"
return HttpResponse("Error: " + error)
