def process_kmer_job():
try:
if skr_config.LOGIN_ENABLED and session.get('logged_in') != True:
return redirect('/login')
parameters = build_seekr_parameters(request)
application.logger.debug(parameters)
t1 = time.perf_counter()
counts, names, comparison_counts, comparison_names, counter = _run_seekr_algorithm(
parameters=parameters)
t2 = time.perf_counter()
application.logger.debug('Running the algorithm took %.3f seconds' %
(t2 - t1))
fixup_counts_warnings = fixup_counts(counts, counter)
if comparison_counts is None:
comparison_counts = counts
comparison_names = names
else:
fixup_comparision_warnings = fixup_counts(comparison_counts,
counter)
kmers = [
''.join(i)
for i in product('AGTC', repeat=parameters['kmer_length'])
]
csv_string = get_kmers_csv(counts=counts, names=names, kmers=kmers)
last_modified = email.utils.formatdate(time.time(), usegmt=True)
headers = {
'Content-Type': 'application/csv',
'Content-Disposition': 'attachment;filename = seekr.csv',
'Content-Length': str(len(csv_string)),
'Last-Modified': last_modified
}
return (csv_string, headers)
except Exception as e:
application.logger.exception('Error in /files/kmers')
#TODO change error from json
return jsonify({'error': "Server_Error: 500"})
def process_pearsons_job():
try:
if skr_config.LOGIN_ENABLED and session.get('logged_in') != True:
return redirect('/login')
parameters = build_seekr_parameters(request)
application.logger.debug('CURRENT METHOD: process_pearsons_job')
t1 = time.perf_counter()
counts, names, comparison_counts, comparison_names, counter = _run_seekr_algorithm(
parameters=parameters)
t2 = time.perf_counter()
application.logger.debug('Running the algorithm took %.3f seconds' %
(t2 - t1))
fixup_counts_warnings = fixup_counts(counts, counter)
if comparison_counts is None:
comparison_counts = counts
comparison_names = names
else:
fixup_comparision_warnings = fixup_counts(comparison_counts,
counter)
pearsons = pearson(counts, comparison_counts)
application.logger.debug("Finished Pearson's. Converting to .csv.")
csv_string = get_pearsons_csv(names, pearsons, comparison_names)
last_modified = email.utils.formatdate(time.time(), usegmt=True)
headers = {
'Content-Type': 'application/csv',
'Content-Disposition': 'attachment;filename = pearsons.csv',
'Content-Length': str(len(csv_string)),
'Last-Modified': last_modified
}
return (csv_string, headers)
except Exception as e:
application.logger.exception('Error in /files/pearsons')
#TODO change error from json
return jsonify({'error': "Server_Error: 500"})
def process_jobs():
try:
if skr_config.LOGIN_ENABLED and session.get('logged_in') != True:
return redirect('/login')
parameters = build_seekr_parameters(request)
application.logger.debug(parameters)
t1 = time.perf_counter()
counts, names, comparison_counts, comparison_names, counter = _run_seekr_algorithm(
parameters=parameters)
t2 = time.perf_counter()
application.logger.debug('Running the algorithm took %.3f seconds' %
(t2 - t1))
if len(names) <= skr_config.MAX_VISUAL_SEQ_LENGTH and len(
comparison_names
) <= skr_config.MAX_VISUAL_SEQ_LENGTH and parameters[
'kmer_length'] <= skr_config.MAX_VISUAL_KMER_LENGTH:
fixup_counts_warnings = fixup_counts(counts, counter)
if comparison_counts is None:
comparison_counts = counts
comparison_names = names
else:
fixup_comparision_warnings = fixup_counts(
comparison_counts, counter)
#reorder according to hierarchical cluster example
if len(counts) > 1:
Z = cluster_vis.cluster_kmers(counts)
ordering = cluster_vis.get_ordering(Z)
ordered_counts = counts[ordering, :]
ordering_int_list = ordering.astype(int).tolist()
ordered_names = [names[i] for i in ordering_int_list]
else:
ordered_counts = counts
ordering_int_list = [0]
ordered_names = names
if len(comparison_counts) > 1:
comparison_Z = cluster_vis.cluster_kmers(comparison_counts)
comparison_ordering = cluster_vis.get_ordering(comparison_Z)
comparison_ordered_counts = comparison_counts[
comparison_ordering, :]
comparison_ordering_int_list = comparison_ordering.astype(
int).tolist()
comparison_ordered_names = [
comparison_names[i] for i in comparison_ordering_int_list
]
else:
comparison_ordered_counts = comparison_counts
comparison_ordering_int_list = [0]
comparison_ordered_names = comparison_names
pearsons = pearson(counts, comparison_counts)
# shorten length of names returned down to 20 characters
new_names = []
for s in names:
if len(s) > skr_config.SEQUENCE_NAME_DISPLAY_LENGTH:
new_names.append(
s[:skr_config.SEQUENCE_NAME_DISPLAY_LENGTH])
else:
new_names.append(s)
names = new_names
new_names = []
for s in comparison_names:
if len(s) > skr_config.SEQUENCE_NAME_DISPLAY_LENGTH:
new_names.append(
s[:skr_config.SEQUENCE_NAME_DISPLAY_LENGTH])
else:
new_names.append(s)
comparison_names = new_names
kmers = [
''.join(i)
for i in product('AGTC', repeat=parameters['kmer_length'])
]
norm_npm = counts
scale_npm = norm_npm.flatten()
mean = np.mean(scale_npm)
z_npm = stats.zscore(scale_npm)
count = 0
for i in z_npm:
if i >= 2:
scale_npm[count] = 2
elif i < -1:
scale_npm[count] = -1
count = count + 1
clean_counts = np.reshape(scale_npm, np.shape(norm_npm))
pearsons = pearsons.round(3)
counts = counts.round(3)
clean_counts = clean_counts.round(3)
pearsons = str(pearsons.tolist())
counts = str(counts.tolist())
clean_counts = str(clean_counts.tolist())
return jsonify({
'user_names': names,
'comparison_names': comparison_names,
'kmer_bins': kmers,
'pearson_matrix': pearsons,
'kmer_matrix': counts,
'kmer_matrix_clean': clean_counts,
'user_cluster': ordering_int_list,
'comparison_cluster': comparison_ordering_int_list,
'user_warnings': fixup_counts_warnings,
'comparison_warnings': fixup_comparision_warnings
})
else:
return jsonify({'visual_flag': True})
except SeekrServerError as e:
application.logger.exception(e)
return jsonify({'error': str(e)})
except Exception as e:
application.logger.exception(e)
return jsonify({'error': '500'})