def remove_sequence(enzyme_type, enzyme_name):
ssn = SSN(enzyme_type)
ssn.load()
if len(list(ssn.graph.nodes)) != 0:
if enzyme_name in list(ssn.graph.nodes):
ssn.graph.nodes.remove(enzyme_name)
ssn.save()
current_app.alignment_queue.enqueue(task_expand_ssn, enzyme_type)
def task_expand_ssn(enzyme_type, log_level=1, max_num=200):
current_app.app_context().push()
aba_blaster = AllByAllBlaster(enzyme_type, log_level=log_level)
aba_blaster.make_blast_db()
ssn = SSN(enzyme_type, aba_blaster=aba_blaster, log_level=log_level)
ssn.load()
ssn.set_status('Checking SSN')
ssn.remove_nonexisting_seqs()
ssn.remove_seqs_marked_with_no_alignments()
biocatdb_seqs = ssn.nodes_not_present(only_biocatdb=True, max_num=max_num)
if len(biocatdb_seqs) != 0:
ssn.clear_position_information()
ssn.set_status('Adding and aligning BioCatDB sequences')
ssn.add_multiple_proteins(biocatdb_seqs)
ssn.save()
current_app.alignment_queue.enqueue(new_expand_ssn_job, enzyme_type)
return
need_alignments = ssn.nodes_need_alignments(max_num=max_num)
if len(need_alignments) != 0:
ssn.clear_position_information()
ssn.set_status('Aligning sequences in SSN')
ssn.add_multiple_proteins(need_alignments)
ssn.save()
current_app.alignment_queue.enqueue(new_expand_ssn_job, enzyme_type)
return
not_present = ssn.nodes_not_present(max_num=max_num)
if len(not_present) != 0:
ssn.clear_position_information()
ssn.set_status('Adding UniRef sequences which are not yet present')
ssn.add_multiple_proteins(not_present)
ssn.save()
current_app.alignment_queue.enqueue(new_expand_ssn_job, enzyme_type)
return
if ssn.db_object.precalculated_vis == {} and len(ssn.graph.nodes) >= 20:
ssn.set_status('Precalculating visualisations')
current_app.preprocess_queue.enqueue(precalculate_job, enzyme_type)
else:
ssn.set_status('Complete')
print(f'- SSN CONSTRUCTION FOR {enzyme_type} IS COMPLETE -')
ssn.db_object.save()