def compute_primers():
# Get the part names.
sequence_name = request.form['sequence_name']
sequence = request.form['sequence'].replace('\n','')
backbone = request.form['backbone']
# Validation checks
if not validate_sequence_characters(sequence):
return error('Sequence contains non-ATGC letters')
if not validate_sequence_length(sequence):
return error('Sequence length has to be at least 100 n.t.')
else:
# Create a SeqRecord object.
part = SeqRecord(Seq(sequence.upper(), alphabet=generic_dna),
name=sequence_name, id=sequence_name)
backbone_part = plasmids[backbone]
p = PrimerDesigner()
p.set_sequences([part, backbone_part])
p.construct_graph()
nodes = p.nodes(data=True)
edges = p.edges(data=True)
protocol = p.pcr_protocol()
return render_template('primers.html',
nodes=nodes,
edges=edges,
protocol=protocol)
def compute_mutagenesis_primers(self):
"""
Using the sequence fragments to be assembled together, computes for
each step the primers that are to be used to assemble the mutated
fragments.
"""
for step, frags in self.fragments.items():
# Run the standard PrimerDesigner protocol.
p = PrimerDesigner()
p.set_sequences(frags)
# Ensure to set the filename attribute.
p.filename = 'step{step}'.format(step=step)
p.construct_graph()
p.compute_assembly_primers()
p.compute_junction_sequencing_primers()
p.compute_pcr_protocol()
self.primer_designers[step] = p
