def check_dimer():
error = None
session_dir = chilli.session(session_parent)
if request.method == 'POST':
infile = os.path.join(session_dir, 'query.fa')
upload_seq = ''
if request.files.has_key('upload_seq'):
upload_seq = request.files['upload_seq'].read()
fasta_seq = ''
if request.form.has_key('fasta_seq'):
fasta_seq = request.form['fasta_seq']
if upload_seq:
seq = upload_seq
elif fasta_seq:
seq = fasta_seq
else:
error = 'Need two or more primer sequences in fasta-format'
return render_template('dimer_index.html', error=error)
fh = open(infile, 'w')
for line in seq.splitlines():
line = line.strip()
if line.startswith('>'):
fh.write("%s\n" % line)
continue
line = re.sub('^[^a-zA-Z]+|[^a-zA-Z]+$', '', line)
line = re.sub('\s', '', line)
fh.write("%s\n" % line)
fh.close()
if len(open(infile).read()) == 0:
error = 'Need two or more primer sequences in fasta-format'
return render_template('batch.html', error = error)
error_or_degenerate = SeqCheck.fasta_format_check(open(infile), err_path='here')
if error_or_degenerate not in ['yes', 'no']:
return render_template('batch.html', error=error_or_degenerate)
mv = float(request.form['mono_conc'])
dv = float(request.form['diva_conc'])
dntp = float(request.form['dntp_conc'])
oligo = float(request.form['oligo_conc'])
align_mode = request.form['mode']
if align_mode == 'HAIRPIN':
hairpin_list = analysis_hairpin(infile, mv, dv, oligo, dntp, align_mode)
return render_template('show_hairpin.html', error=error, hairpin_list=hairpin_list)
else:
dimer_list = analysis_dimer(infile, mv, dv, oligo, dntp, align_mode)
return render_template('show_dimer.html', error=error, dimer_list=dimer_list)
return render_template('dimer_index.html', error=error)
def check_infile(options):
'''Check and return Oligos'''
err_or_degenerate = SeqCheck.fasta_format_check(options.infile)
if err_or_degenerate in ['yes', 'no']:
global degenerate
degenerate = err_or_degenerate
else:
print2stderr(err_or_degenerate)
options.infile.seek(0)
if degenerate == 'no':
oligos = FastaFormatParser.parse(options.infile)
else:
oligos = DegenerateSeqConvetor.convert(FastaFormatParser.parse(options.infile))
options.infile.close()
return oligos
def check_infile(options):
'''Check and return Oligos'''
err_or_degenerate = SeqCheck.fasta_format_check(options.infile)
if err_or_degenerate in ['yes', 'no']:
global degenerate
degenerate = err_or_degenerate
else:
print2stderr(err_or_degenerate)
options.infile.seek(0)
if degenerate == 'no':
oligos = FastaFormatParser.parse(options.infile)
else:
oligos = DegenerateSeqConvetor.convert(
FastaFormatParser.parse(options.infile))
options.infile.close()
return oligos
def single_mode():
"""Single mode"""
error = None
session_dir = chilli.session(session_parent)
if request.method == 'POST':
database = request.form['db_selected']
db_list = [os.path.join(MFEprimerDB, db) for db in database.split(':')]
infile = os.path.join(session_dir, 'query.fa')
fh = open(infile, 'w')
seq_sn = 1
seq_list = []
while request.form.has_key("seq%d" % seq_sn):
seq = request.form["seq%d" % seq_sn]
seq = re.sub('^[^a-zA-Z]+|[^a-zA-Z]+$', '', seq) # Remove additional chars, such as 5'- 3'-
seq = re.sub('\s', '', seq) # Remove spaces in sequence. Thanks anonymous reviewers.
if seq:
seq_list.append(seq)
fh.write(">Seq%s\n%s\n" % (seq_sn, seq))
seq_sn += 1
fh.close()
if len(seq_list) < 2:
error = 'Need two or more primer sequences'
return render_template('index.html', error=error)
error_or_degenerate = SeqCheck.fasta_format_check(open(infile), err_path='here')
if error_or_degenerate in ['yes', 'no']:
degenerate = error_or_degenerate
else:
return render_template('index.html', error=error_or_degenerate)
Tm_upper_limit = float(request.form['Tm_upper_limit'])
Tm_lower_limit = float(request.form['Tm_lower_limit'])
size_upper_limit = int(request.form['size_upper_limit'])
size_lower_limit = int(request.form['size_lower_limit'])
if size_lower_limit < 0 or size_upper_limit > 100000:
error = 'Size range should be in [0, 100000]'
return render_template('index.html', error=error)
ppc_lower_limit = float(request.form['ppc_lower_limit'])
if ppc_lower_limit < 0 or ppc_lower_limit > 100:
error = 'PPC lower cutoff should be in (0, 100)'
return render_template('index.html', error=error)
mv = float(request.form['mono_conc'])
dv = float(request.form['diva_conc'])
dntp = float(request.form['dntp_conc'])
oligo = float(request.form['oligo_conc'])
session['db_selected'] = ':'.join([os.path.basename(str(db)) for db in db_list])
options = OptionCreator(db_list,
infile,
Tm_upper_limit,
Tm_lower_limit,
size_upper_limit,
size_lower_limit,
ppc_lower_limit,
mv,
dv,
dntp,
oligo,
degenerate,
)
start_time = time.time()
amp_list, oligos = MFEprimer.process_primer(options, session_dir)
detail, size_dict, tm_dict, dg_dict = format_output_primer(amp_list, oligos, options, start_time, session_dir)
if len(detail) > hist_cutoff:
size_hist_keys = size_hist.keys()
size_hist_keys.sort(reverse=True)
for size, num in size_dict.items():
for hist_key in size_hist_keys:
if int(size) > hist_key:
break
size_hist[hist_key] += num
tm_hist_keys = tm_hist.keys()
tm_hist_keys.sort(reverse=True)
for tm, num in tm_dict.items():
for hist_key in tm_hist_keys:
if float(tm) > hist_key:
break
tm_hist[hist_key] += num
dg_hist_keys = dg_hist.keys()
dg_hist_keys.sort(reverse=False)
for dg, num in dg_dict.items():
for hist_key in dg_hist_keys:
if float(dg) < float(hist_key):
break
dg_hist[hist_key] += num
new_dg_hist = {}
for key, value in dg_hist.items():
new_dg_hist[str(key)] = value
database = ', '.join([os.path.basename(db).capitalize() for db in options.database])
oligos = format_oligos(oligos, options)
elapsed_time = time.time() - start_time
if elapsed_time < 1:
print_elapsed_time = '%.2f s' % elapsed_time
else:
print_elapsed_time = '%s m %s s' % chilli.seconds2min_sec(int(elapsed_time))
return render_template('primer_output.html', options=options, database=database,
oligos=oligos, amp_num=len(amp_list), time_used=print_elapsed_time,
date=chilli.format_show_time(), citation=Citation, detail=detail,
session_dir=session_dir, size_hist=size_hist, tm_hist=tm_hist, dg_hist=new_dg_hist,
max_size_num = max([num for num in size_hist.values()]),
max_tm_num = max([num for num in tm_hist.values()]),
max_dg_num = max([num for num in dg_hist.values()]),
)
return redirect(url_for('root'))
def batch_mode():
"""batch mode"""
error = None
session_dir = chilli.session(session_parent)
if request.method == 'POST':
species_list = request.form.getlist('db_selected')
if len(species_list) == 0:
error = 'Need select database first'
return render_template('batch.html', error = error)
db_type_list = [db_type.lower() for db_type in request.form['db_type'].split(':')]
session['db_type'] = request.form['db_type']
session['species_list'] = species_list
db_list = []
for species in species_list:
for db_type in db_type_list:
db = '%s.%s' % (species, db_type)
db = db.lower()
if db in g.db_name_dict:
full_db = os.path.join(MFEprimerDB, g.db_name_dict[db])
db_list.append(full_db)
db_list.sort()
infile = os.path.join(session_dir, 'query.fa')
upload_seq = ''
if request.files.has_key('upload_seq'):
upload_seq = request.files['upload_seq'].read()
fasta_seq = ''
if request.form.has_key('fasta_seq'):
fasta_seq = request.form['fasta_seq']
if upload_seq:
seq = upload_seq
elif fasta_seq:
seq = fasta_seq
else:
error = 'Need two or more primer sequences in fasta-format'
return render_template('batch.html', error = error)
fh = open(infile, 'w')
for line in seq.splitlines():
line = line.strip()
if line.startswith('>'):
fh.write("%s\n" % line)
continue
line = re.sub('^[^a-zA-Z]+|[^a-zA-Z]+$', '', line)
line = re.sub('\s', '', line)
fh.write("%s\n" % line)
fh.close()
if len(open(infile).read()) == 0:
error = 'Need two or more primer sequences in fasta-format'
return render_template('batch.html', error = error)
error_or_degenerate = SeqCheck.fasta_format_check(open(infile), err_path='here')
if error_or_degenerate in ['yes', 'no']:
degenerate = error_or_degenerate
else:
return render_template('batch.html', error=error_or_degenerate)
Tm_upper_limit = float(request.form['Tm_upper_limit'])
Tm_lower_limit = float(request.form['Tm_lower_limit'])
size_upper_limit = int(request.form['size_upper_limit'])
size_lower_limit = int(request.form['size_lower_limit'])
if size_lower_limit < 0 or size_upper_limit > 100000:
error = 'Size range should be in [0, 100000]'
return render_template('batch.html', error = error)
ppc_lower_limit = float(request.form['ppc_lower_limit'])
if ppc_lower_limit < 0 or ppc_lower_limit > 100:
error = 'PPC lower cutoff should in (0, 100)'
return render_template('batch.html', error = error)
mv = float(request.form['mono_conc'])
dv = float(request.form['diva_conc'])
dntp = float(request.form['dntp_conc'])
oligo = float(request.form['oligo_conc'])
options = OptionCreator(db_list,
infile,
Tm_upper_limit,
Tm_lower_limit,
size_upper_limit,
size_lower_limit,
ppc_lower_limit,
mv,
dv,
dntp,
oligo,
degenerate,
)
start_time = time.time()
session_key = os.path.basename(session_dir)
args = ['database', 'infile', 'dg_stop', 'dg_start', 'tm_stop', 'tm_start', 'size_stop', 'size_start', 'ppc', 'mono_conc', 'diva_conc', 'dntp_conc', 'oligo_conc', 'degenerate', 'k_value']
job_file = create_jobs(options, args, session_key)
return render_template('results_notice.html', session_key=session_key, job_file=job_file + '.zip', status='Submitted')
return redirect(url_for('batch'))