diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/correlation/pre_computes.py | 44 |
1 files changed, 40 insertions, 4 deletions
diff --git a/wqflask/wqflask/correlation/pre_computes.py b/wqflask/wqflask/correlation/pre_computes.py index 95047fc7..eb089a03 100644 --- a/wqflask/wqflask/correlation/pre_computes.py +++ b/wqflask/wqflask/correlation/pre_computes.py @@ -4,6 +4,7 @@ import hashlib from pathlib import Path from base.data_set import query_table_timestamp +from base.webqtlConfig import TEXTDIR from base.webqtlConfig import TMPDIR from json.decoder import JSONDecodeError @@ -168,13 +169,48 @@ def get_datasets_data(base_dataset, target_dataset_data): return (target_results, base_results) -def fetch_text_file(dataset_name, text_dir, conn): + +def fetch_text_file(dataset_name, conn, text_dir=TEXTDIR): """fetch textfiles with strain vals if exists""" + with conn.cursor() as cursor: query = 'SELECT Id, FullName FROM ProbeSetFreeze WHERE Name = "%s"' % dataset_name cursor.execute(query) results = cursor.fetchone() if (results): - for file in os.listdir(text_dir): - if file.startswith(f"ProbeSetFreezeId_{results[0]}_"): - return os.path.join(text_dir, file) + try: + for file in os.listdir(text_dir): + if file.startswith(f"ProbeSetFreezeId_{results[0]}_"): + return os.path.join(text_dir, file) + except FileNotFoundError: + pass + + +def read_text_file(sample_dict, file_path): + + def parse_line_csv(line): + return_list = line.split('","') + return_list[-1] = return_list[-1][:-2] + return_list[0] = return_list[0][1:] + return return_list + + def __fetch_id_positions__(all_ids, target_ids): + _vals = [] + _posit = [0] # alternative for parsing + + for (idx, strain) in enumerate(all_ids, 1): + if strain in target_ids: + _vals.append(target_ids[strain]) + _posit.append(idx) + + else: + _vals.append("") # todo;modify x_vals to take string rust + + return (_posit, _vals) + with open(file_path, "r") as file_handler: + all_ids = file_handler.readline() + _posit, sample_vals = __fetch_id_positions__( + parse_line_csv(all_ids)[1:], sample_dict) + + return (sample_vals, [",".join(parse_line_csv(line)) + for line in file_handler.readlines()]) |