def main():
global_var.init()
args = make_args()
check_environments(args)
check_templates(args)
check_qPCR(args)
run(args)
}
# generate primers
if id not in primers:
primers[id] = {}
primers[id]['PRIMER_PAIR_NUM_RETURNED'] = rank + 1
primers[id][f'PRIMER_PAIR_{rank}_PENALTY'] = 0
primers[id][f'PRIMER_LEFT_{rank}_SEQUENCE'] = seq_F
primers[id][f'PRIMER_RIGHT_{rank}_SEQUENCE'] = seq_R
primers[id][f'PRIMER_LEFT_{rank}'] = [-1, len(seq_F)]
primers[id][f'PRIMER_RIGHT_{rank}'] = [-1, len(seq_R)]
primers[id][f'PRIMER_LEFT_{rank}_TM'] = primer3.calcTm(
transform_degenerate(seq_F))
primers[id][f'PRIMER_RIGHT_{rank}_TM'] = primer3.calcTm(
transform_degenerate(seq_R))
primers[id][f'PRIMER_LEFT_{rank}_GC_PERCENT'] = calculate_GC(
transform_degenerate(seq_F))
primers[id][f'PRIMER_RIGHT_{rank}_GC_PERCENT'] = calculate_GC(
transform_degenerate(seq_R))
primers[id][f'PRIMER_PAIR_{rank}_PRODUCT_SIZE'] = -1
primers[id]['SEQUENCE_RELATIVE_TARGET_START'] = 0
return primers
if __name__ == "__main__":
global_var.init()
with open('tests/_internal_/query_check') as f:
primers = make_primers(f.read())
print(json.dumps(primers, 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)
