def add_sequence(request, pk):
sl = SequenceListing.objects.get(pk=pk)
if request.method == 'POST':
organism = request.POST.get('organism')
form = SequenceForm(request.POST)
if form.is_valid():
cd = form.cleaned_data
raw_residues = cd['residues']
sequence_instance = Sequence(sequenceListing = sl,
length = len(cd['residues']),
moltype = cd['moltype'],
residues = cd['residues']
)
sequence_instance.save()
feature_source_helper(sequence_instance, organism)
# create a note qualifier to indicate the a formula if applicable
if '(' in raw_residues:
value_for_note = 'note'
if cd['moltype'] == 'AA':
value_for_note = 'NOTE'
feature_instance = Feature.objects.filter(sequence = sequence_instance)[0]
note_qualifier_instance = Qualifier.objects.create(feature=feature_instance,
qualifierName=value_for_note,
qualifierValue=raw_residues)
note_qualifier_instance.save()
return HttpResponseRedirect(reverse('sequencelistings:detail', args=(pk,)))
else:
form = SequenceForm()
return render(request, 'sequencelistings/add_seq.html', {'form': form, 'pk': pk, 'seql': sl})
def sequence(request, pk, spk):
seq = Sequence.objects.get(pk=spk)
form = SequenceForm(
instance=seq,
# sn = seq.sequenceName,
initial={
'organism': seq.getOrganism(),
'sequenceName': seq.sequenceName
})
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
return render(
request, 'sequencelistings/sequence.html', {
'form': form,
'seq': seq,
'featureFormDic': featureFormDic,
'qualifierFormDic': qualifierFormDic,
})
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 index():
form = SequenceForm()
details = []
if form.validate_on_submit():
for seq in re.findall(r'[ACGT]{23}', form.sequence.data.upper()):
scores = calculator.calculate_sequence(seq)
details.append({"sequence": seq, "scores": scores})
if form.csv.data:
return render_csv(details)
return render_template('index.html', form=form, details=details)
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})
def add_sequence(request, pk):
sl = SequenceListing.objects.get(pk=pk)
currentSeqIdNo = len(sl.sequence_set.all()) + 1
currentSequenceName = 'seq_%i' % currentSeqIdNo
if request.method == 'POST':
form = SequenceForm(request.POST)
if form.is_valid():
print 'form is valid'
cd = form.cleaned_data
raw_residues = cd['residues']
sequence_instance = Sequence(sequenceListing=sl,
sequenceName=cd['sequenceName'],
length=len(cd['residues']),
moltype=cd['moltype'],
residues=cd['residues'],
skipped=cd['skipped'])
sequence_instance.save()
organism = request.POST.get('organism')
qualmoltype = request.POST.get('qualmoltype')
feature_source_helper(sequence_instance, organism, qualmoltype)
# create a note qualifier to indicate the a formula if applicable
if '(' in raw_residues:
value_for_note = 'note'
if cd['moltype'] == 'AA':
value_for_note = 'NOTE'
feature_instance = Feature.objects.filter(
sequence=sequence_instance)[0]
note_qualifier_instance = Qualifier.objects.create(
feature=feature_instance,
qualifierName=value_for_note,
qualifierValue=raw_residues)
note_qualifier_instance.save()
return HttpResponseRedirect(
reverse('sequencelistings:edit_seql', args=(pk, )))
else:
print 'Form not valid.'
else:
form = SequenceForm(initial={'sequenceName': currentSequenceName})
return render(request, 'sequencelistings/add_seq.html', {
'form': form,
'pk': pk,
'seql': sl
})
def manual_add(request):
"""Add a fragment manually"""
if request.method == 'GET':
meta = MetaForm(request.GET)
seq = SequenceForm(request.GET)
if meta.is_valid() and seq.is_valid():
record = SeqRecord( seq.cleaned_data['seq'],
name=meta.cleaned_data['name'],
id=meta.cleaned_data['name'],
description=meta.cleaned_data['desc'])
Gene.add(record, 'MN', request.user)
return JsonResponse('OK');
#figure out what the errors where
errors = meta.errors
errors.update(seq.errors)
return JsonResponse(errors, ERROR)
raise Http404
def manual_add(request):
"""Add a fragment manually"""
if request.method == 'GET':
meta = MetaForm(request.GET)
seq = SequenceForm(request.GET)
if meta.is_valid() and seq.is_valid():
record = SeqRecord( seq.cleaned_data['seq'],
name=meta.cleaned_data['name'],
id=meta.cleaned_data['name'],
description=meta.cleaned_data['desc'])
Gene.add(record, 'MN', request.user)
return JsonResponse('OK');
#figure out what the errors where
errors = meta.errors
errors.update(seq.errors)
return JsonResponse(errors, ERROR)
raise Http404
def manual_form(request):
t = loader.get_template('fragment/MNform.html')
meta = MetaForm()
seq = SequenceForm()
c = RequestContext(request, { 'meta': meta, 'seq': seq,
'title':'Manually add a Fragment',
'action': 'import/manual/add/',})
return HttpResponse(t.render(c))
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
return render(request, 'sequencelistings/sequence.html', {'form': form, 'seq': seq,
'featureFormDic': featureFormDic,
'qualifierFormDic': qualifierFormDic,})
