def sequence(request, pk, spk):
seq = Sequence.objects.get(pk=spk)
form = SequenceForm(instance=seq, initial={'organism': seq.getOrganism()})
form.organism = seq.getOrganism()
featureFormDic = {}
qualifierFormDic = {}
for f in seq.feature_set.all():
featureFormDic[f] = FeatureForm(instance=f, mt=seq.moltype, initial={'featureKey': f.featureKey})
qualifierFormList = []
for q in f.qualifier_set.all():
qualifierFormList.append(QualifierForm(feature=f,
instance=q,
initial={'qualifierName': q.qualifierName}))
qualifierFormDic[f] = qualifierFormList
# if request.method == 'POST':
# if form.is_valid():
# cd = form.cleaned_data
#
# fk = cd['featureKey']
# fl = cd['location']
# f = Feature.objects.create(sequence=seq, featureKey=fk, location=fl)
# f.save()
# return HttpResponseRedirect(reverse('sequencelistings:detail', args=(pk,)))
# else:
# form = FeatureForm(mt=seq.moltype)
return render(request, 'sequencelistings/sequence.html', {'form': form, 'seq': seq,
'featureFormDic': featureFormDic,
'qualifierFormDic': qualifierFormDic,})
def add_sequence(request, pk):
# print 'add_sequence invoked'
if request.method == 'POST':
organism = request.POST.get('organism')
form = SequenceForm(request.POST)
if form.is_valid():
sl = SequenceListing.objects.get(pk=pk)
cd = form.cleaned_data
sequence_instance = Sequence(sequenceListing = sl,
length = len(cd['residues']),
moltype = cd['moltype'],
residues = cd['residues']
)
sequence_instance.save()
value_for_source = 'source'
if cd['moltype'] == 'AA':
value_for_source = 'SOURCE'
value_for_organism = 'organism'
if cd['moltype'] == 'AA':
value_for_organism = 'ORGANISM'
value_for_moltype = 'mol_type'
if cd['moltype'] == 'AA':
value_for_moltype = 'MOL_TYPE'
feature_instance = Feature.objects.create(sequence=sequence_instance,
featureKey=value_for_source,
location='1..%s' % sequence_instance.length)
feature_instance.save()
organism_qualifier_instance = Qualifier.objects.create(feature=feature_instance,
qualifierName=value_for_organism,
qualifierValue=organism)
organism_qualifier_instance.save()
mol_type_qualifier_instance = Qualifier.objects.create(feature=feature_instance,
qualifierName=value_for_moltype,
qualifierValue=util.MOL_TYPE_QUALIFIER_VALUES[cd['moltype']])
mol_type_qualifier_instance.save()
return HttpResponseRedirect(reverse('sequencelistings:detail', args=(pk,)))
else:
form = SequenceForm()
return render(request, 'sequencelistings/add_seq.html', {'form': form, 'pk': pk})
