def function(seq, category, prefix, suffix, enzymes, with_intron):
pcrs, seq = domesticate(seq, category, prefix, suffix, enzymes,
with_intron)
protocol = write_domestication_protocol(pcrs)
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(seq, category, prefix, suffix, enzymes,
with_intron)[1]
response = HttpResponse(convert_to_sbol(seq),
content_type='text/xml')
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(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 xtest_daniels_promoter(self):
fasta_path = os.path.join(TEST_DATA, 'prVvbHLH35v2.fa')
seqrec = SeqIO.read(fasta_path, 'fasta')
dom_seq = domesticate(seqrec, '01-02-03-11-12 (PROM+UTR+ATG)',
'GGAG', 'AATG')[1]
print len(dom_seq), seqrec.seq.upper()
print len(dom_seq), dom_seq.seq
assert ('GGAG', 'AATG') == get_prefix_and_suffix(dom_seq.seq, 'BsaI')
def domestication_view_add(request):
context = RequestContext(request)
context.update(csrf(request))
request_data = request.POST
# request_data
seq = request_data['seq']
category = request_data['category']
prefix = request_data['prefix']
suffix = request_data['suffix']
seq_name = request_data['seq_name']
name = request_data['name']
with_intron = bool(int(request_data['with_intron']))
if category == 'None':
category_name = 'Other'
else:
category_name = CATEGORIES[category][0]
seq = SeqRecord(Seq(seq), id=seq_name, name=seq_name)
seq = domesticate(seq, category, prefix, suffix, with_intron)[1]
temp_fhand = NamedTemporaryFile(prefix='{0}.'.format(seq.id),
suffix='.gb')
temp_fhand.write(seq.format('gb'))
temp_fhand.flush()
temp_fhand.seek(0)
props = {'Description': [request_data['description']],
'Reference': [request_data['reference']]}
try:
feature = add_feature(name=name, type_name=category_name,
vector=DOMESTICATED_VECTOR, genbank=temp_fhand,
props=props, owner=request.user, is_public=False)
except IntegrityError as error:
print error
if 'feature already in db' in str(error):
# TODO choose a template
return render_to_response('feature_exists.html',
{},
context_instance=RequestContext(request))
else:
return HttpResponseServerError()
except Exception as error:
print error
return HttpResponseServerError()
# if everithing os fine we show the just added feature
return redirect(feature.url)
def test_get_prefix_and_suffix(self):
'it tests get a suffix and prefix test'
gb_path = os.path.join(TEST_DATA, 'pAn11_uniq.gb')
seq = SeqIO.read(gb_path, 'gb')
seq = seq.seq
assert ('AATG', 'GCTT') == get_prefix_and_suffix(seq, 'BsaI')
fasta_path = os.path.join(TEST_DATA, 'seq.fasta')
seq = SeqIO.read(fasta_path, 'fasta')
seq = seq.seq
assert ('TGGA', 'AATG') == get_prefix_and_suffix(seq, 'BsaI')
# no rec_sites
fasta_path = os.path.join(TEST_DATA, 'seq2.fasta')
seq = SeqIO.read(fasta_path, 'fasta')
seq = seq.seq
assert (None, None) == get_prefix_and_suffix(seq, 'BsaI')
# no rec_sites
fasta_path = os.path.join(TEST_DATA, 'seq_with_intron.fasta')
seqrec = SeqIO.read(fasta_path, 'fasta')
dom_seq = domesticate(seqrec, None, 'CCAT', 'AATG')[1]
assert ('CCAT', 'AATG') == get_prefix_and_suffix(dom_seq.seq, 'BsaI')
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)
