def function(seq, category, prefix, suffix, enzymes, with_intron):
seq = domesticate_for_synthesis(seq, category, prefix, suffix, enzymes,
with_intron)[0]
protocol = write_synthesis_protocol(seq)
response = HttpResponse(protocol, content_type='text/plain')
response['Content-Disposition'] = 'attachment; filename="protocol.txt"'
return response
def function(seq, category, prefix, suffix, enzymes, with_intron):
seq = domesticate_for_synthesis(seq, category, prefix, suffix, enzymes,
with_intron)[1]
response = HttpResponse(convert_to_sbol(seq),
content_type='xml/plain')
response['Content-Disposition'] = 'attachment; '
response['Content-Disposition'] += 'filename="{0}.xml"'.format(seq.id)
return response
def function(seq, category, prefix, suffix, enzymes, with_intron):
seq = domesticate_for_synthesis(seq, category, prefix, suffix, enzymes,
with_intron)[1]
response = HttpResponse(seq.format('genbank'),
content_type='text/plain')
response['Content-Disposition'] = 'attachment; '
response['Content-Disposition'] += 'filename="{0}.gb"'.format(seq.id)
return response
def _domestication_view(request, kind):
context = RequestContext(request)
context.update(csrf(request))
if request.method == 'POST':
request_data = request.POST
elif request.method == 'GET':
request_data = request.GET
else:
request_data = None
if request_data:
form = DomesticationForm(request_data, request.FILES)
# do domestication
if form.is_valid():
seq = form.cleaned_data['seq']
if seq is None:
seq = form.cleaned_data['residues']
category = form.cleaned_data.get('category', None)
enzymes = form.cleaned_data.get('enzymes', None)
if category is None:
prefix = form.cleaned_data.get('prefix')
suffix = form.cleaned_data.get('suffix')
else:
try:
prefix = CATEGORIES[category][1]
suffix = CATEGORIES[category][2]
except KeyError:
prefix = CRYSPER_CATEGORIES[category][1]
suffix = CRYSPER_CATEGORIES[category][2]
with_intron = form.cleaned_data['with_intron']
with_intron_str = '1' if with_intron else '0'
if kind == 'domestication':
try:
pcr = domesticate(seq, category, prefix, suffix, enzymes,
with_intron)[0]
except RuntimeError as error:
return render_to_response('goldenbraid_info.html',
{'title': 'Can not domesticate sequence',
'info': error},
context_instance=RequestContext(request))
return render_to_response('domestication_result.html',
{'category': category,
'prefix': prefix,
'suffix': suffix,
'pcrs': pcr,
'seq': str(seq.seq),
'seq_name': seq.name,
'enzymes': enzymes,
'with_intron': with_intron_str},
context_instance=RequestContext(request))
elif kind == 'synthesis':
try:
seq_for_syn, prepared_seq = domesticate_for_synthesis(seq,
category,
prefix,
suffix,
enzymes,
with_intron)
except RuntimeError as error:
return render_to_response('goldenbraid_info.html',
{'title': 'Can not domesticate sequence',
'info': error},
context_instance=RequestContext(request))
return render_to_response('synthesis_result.html',
{'category': category,
'prefix': prefix,
'suffix': suffix,
'seq_syn': seq_for_syn,
'seq': str(seq.seq),
'seq_name': prepared_seq.name,
'enzymes': enzymes,
'with_intron': with_intron_str},
context_instance=RequestContext(request))
else:
form = DomesticationForm()
context['form'] = form
context['kind'] = kind
template = 'domestication_template.html'
content_type = None
return render_to_response(template, context, content_type=content_type)