def get_expr_info():
if request.method == 'POST':
info = request.form['info']
info = json.loads(info)
table = info['table']
map_groupA = info['groupA']
map_groupB = info['groupB']
groupA = map_sample(map_groupA, map_dict=web2db_dict)
groupB = map_sample(map_groupB, map_dict=web2db_dict)
gene_str = info['gene_name']
gene_ids = re.split(r'[\s,]', gene_str.strip())
if len(gene_ids) > 10:
return jsonify({'msg': 'query gene number not allowed > 10'})
query_header, query_data = get_expr_table(table, gene_ids, groupA,
groupB, map_groupA,
map_groupB)
if not query_data:
return jsonify(
{'msg': 'not search {0} in database!'.format(query_header)})
return jsonify({
'msg': 'ok',
'headData': query_header,
'bodyData': query_data
})
def test_mapSample():
db2web_dict, web2db_dict = get_map()
samples = get_samples_by_table(table='snp_mRNA_table', type='snp')
test_web_sets = ['159_9_CS_P_2', '196_2_D_P', 'W3_14LL']
test_db_sets = 'G097_0204_32bei1'
web_samples = map_sample(samples, db2web_dict)
db_samples = map_sample(test_web_sets, web2db_dict)
assert test_db_sets in db_samples
assert random.choice(test_web_sets) in web_samples
def select_file_by_plot():
filename = request.args.get('file', '')
if filename:
samples = get_samples_by_table(filename, type='snp')
samples = map_sample(samples, db2web_dict)
if not samples:
return jsonify({'msg': 'error'})
return jsonify({'msg': samples})
return jsonify({'msg': 'error'})
def generate_snp_plot():
if request.method == 'POST':
info = json.loads(request.form['info'])
table = info['table']
groupA = map_sample(info['groupA'], map_dict=web2db_dict)
groupB = map_sample(info['groupB'], map_dict=web2db_dict)
groupA_name = info['customGroupA']
groupB_name = info['customGroupB']
chrom = info['chrom']
filename = "%svs%s" % (groupA_name, groupB_name)
cmd, groupA_len, groupB_len = get_cmd_by_regin(table,
groupA,
groupB,
chrom=chrom,
get_all=True)
query_data = calculate_table(cmd,
groupA_len,
groupB_len,
filename,
output=True,
chrom=chrom)
msg = run_snpplot_script(
filepath=os.path.join(SNP_INDEX_PATH,
'_'.join([groupA_name,
groupB_name]), query_data),
outdir=os.path.join(
SNP_INDEX_PATH, '_'.join([groupA_name, groupB_name]),
'vs'.join([groupA_name, groupB_name]) + '_plot'))
files = glob.glob(
os.path.join(SNP_INDEX_PATH, '_'.join([groupA_name, groupB_name]),
'vs'.join([groupA_name, groupB_name]) + '_plot') +
'/*png')
files_short = [each.rsplit('/', 1)[1] for each in files]
path = os.path.join(RENDER_PATH, '_'.join([groupA_name, groupB_name]),
'vs'.join([groupA_name, groupB_name]) + '_plot')
return jsonify({
'msg':
query_data,
'name':
'vs'.join([groupA_name, groupB_name]),
'files': [os.path.join(path, each) for each in files_short]
})