Mercurial > repos > ieguinoa > ena_upload

comparison dump_yaml.py @ 2:2f7a70c0d3ab draft default tip

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author ieguinoa
date Mon, 21 Feb 2022 14:22:53 +0000
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1:9681a9180730 2:2f7a70c0d3ab
1 import sys
2 import yaml
3
4 def fetch_table_data(table_path):
5 data_dict = {}
6 with open(table_path) as table_to_load:
7 # load headers
8 headers = table_to_load.readline().strip('\n').split('\t')
9 row_id = 0
10 for line in table_to_load.readlines():
11 # print(line)
12 line_data = line.strip('\n').split('\t')
13 row_dict = {}
14 for col_num in range(len(headers)):
15 col_name = headers[col_num]
16 row_dict[col_name] = line_data[col_num]
17 data_dict[row_id] = row_dict
18 row_id += 1
19 return data_dict
20
21 all_data_dict = {}
22 print('YAML -------------')
23 studies_table_path = sys.argv[1]
24 table_data = fetch_table_data(studies_table_path)
25 all_data_dict['ENA_study'] = table_data
26 samples_table_path = sys.argv[2]
27 table_data = fetch_table_data(samples_table_path)
28 all_data_dict['ENA_sample'] = table_data
29 experiments_table_path = sys.argv[3]
30 table_data = fetch_table_data(experiments_table_path)
31 all_data_dict['ENA_experiment'] = table_data
32 runs_table_path = sys.argv[4]
33 table_data = fetch_table_data(runs_table_path)
34 all_data_dict['ENA_run'] = table_data
35 # print(all_data_dict)
36 print(yaml.dump(all_data_dict))
37 print('YAML -------------')