def dbdownload(template):
web_config = load()
db_dir = web_config['templates_directory']
result = os.popen(f'cut -f 1,2 {db_dir}/{template}.fai').read()
response = make_response(result)
response.headers[
"Content-Disposition"] = f"attachment; filename={template}.fai"
response.headers["Content-type"] = "application/octet-stream"
return response
def dbselect():
web_config = load()
dbs_in_select = {}
for (template, meta) in web_config['templates'].items():
(desc, group, ids) = (meta['description'], meta['group'], meta['IDs'])
if group not in dbs_in_select:
dbs_in_select[group] = {}
if template not in dbs_in_select[group]:
dbs_in_select[group][template] = {}
dbs_in_select[group][template]['desc'] = desc
dbs_in_select[group][template]['IDs'] = ids
return json.dumps(dbs_in_select, indent=4)
def run():
################### init #############################
web_config = load()
global_var.init()
db_dir = web_config['templates_directory']
################### Design primers ###################
query_string = request.form['query']
dbs = [db_dir + '/' + x for x in request.form['selected_dbs'].split(',')]
if request.form['app-type'] == 'check':
primers = make_primers.make_primers(query=query_string)
if 'error' in primers:
return json.dumps(
{
'error':
'<p>' + primers['error'] + '</p>' +
'<p>Your inputs might be invalid; Check the \
<a href="javascript:void(0)" data-toggle="modal" data-target="#input-help">manual</a> carefully \
to ensure that your inputs are in correct formats</p>'
},
indent=4)
else:
if request.form['app-type'] == 'design':
primer_num_return = request.form['retain']
else:
primer_num_return = request.form['primer_num_return']
if make_sites.judge_input_type(query_string) == 'pos':
sites = make_sites.build_by_pos(query=query_string, template_file=dbs[0], primer_type=request.form['region_type'], \
primer_num_return=int(primer_num_return), size_min=int(request.form['product_size_min']), \
size_max=int(request.form['product_size_max']), pick_internal=bool(int(request.form['pick_internal'])), \
use_junction=bool(int(request.form['junction'])) )
else:
sites = make_sites.build_by_seq(query=query_string, primer_type=request.form['region_type'], \
primer_num_return=int(primer_num_return), size_min=int(request.form['product_size_min']), \
size_max=int(request.form['product_size_max']), pick_internal=bool(int(request.form['pick_internal'])))
if 'error' in sites:
return json.dumps(
{
'error':
'<p>' + sites['error'] + '</p>' +
'<p>Your inputs might be invalid; Check the \
<a href="javascript:void(0)" data-toggle="modal" data-target="#input-help">manual</a> carefully \
to ensure that your inputs are in correct formats</p>'
},
indent=4)
primers = design_primer.multiple(sites,
cpu=web_config['cpu'],
monitor=False)
################### Checking specificity #############
if request.form['app-type'] != 'design':
primers = run_blast.run_blast_parallel(primers=primers, dbs=dbs, cpu=web_config['cpu'],\
checking_size_max=int(request.form['checking_size_max']), checking_size_min=int(request.form['checking_size_min']), \
report_amplicon_seq=bool(int(request.form['report_amplicon_seqs'])), Tm_diff=int(request.form['Tm_diff']), \
use_3_end=bool(int(request.form['use_3_end'])), monitor=False)
primers = sort_primers.sort_rank(primers=primers, dbs=dbs, max_num_return=int(request.form['retain']), \
use_isoforms=bool(int(request.form['isoform'])) )
################### Checking multiplex ###############
dimers = {}
if int(request.form['multiplex']) == 1:
dimers = multiplex.extract_fake_pair(primers,
Tm_diff=int(
request.form['Tm_diff']),
cpu=web_config['cpu'],
monitor=False)
################### Output #########################
global_var.current_task = 'finish'
return json.dumps({'meta':{'mode':request.form['app-type'], 'dbs':dbs, 'region_type': request.form['region_type'], \
'check_multiplex': bool(int(request.form['multiplex']))}, 'primers':primers, 'dimers':dimers}, indent=4)
def dbinfo():
web_config = load()
return json.dumps(web_config['templates'], indent=4)