Mercurial > repos > iuc > ena_upload

comparison dump_yaml.py @ 7:ae2d35b56645 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 9961f24acebb17f837238df6541e1af59df1163b"
author iuc
date Thu, 24 Feb 2022 18:20:02 +0000
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6:1c79c7ee82c4 7:ae2d35b56645
1 import sys
2
3 import yaml
4
5
6 def fetch_table_data(table_path):
7 data_dict = {}
8 with open(table_path) as table_to_load:
9 # load headers
10 headers = table_to_load.readline().strip('\n').split('\t')
11 row_id = 0
12 for line in table_to_load.readlines():
13 # print(line)
14 line_data = line.strip('\n').split('\t')
15 row_dict = {}
16 for col_num in range(len(headers)):
17 col_name = headers[col_num]
18 row_dict[col_name] = line_data[col_num]
19 data_dict[row_id] = row_dict
20 row_id += 1
21 return data_dict
22
23
24 all_data_dict = {}
25 print('YAML -------------')
26 studies_table_path = sys.argv[1]
27 table_data = fetch_table_data(studies_table_path)
28 all_data_dict['ENA_study'] = table_data
29 samples_table_path = sys.argv[2]
30 table_data = fetch_table_data(samples_table_path)
31 all_data_dict['ENA_sample'] = table_data
32 experiments_table_path = sys.argv[3]
33 table_data = fetch_table_data(experiments_table_path)
34 all_data_dict['ENA_experiment'] = table_data
35 runs_table_path = sys.argv[4]
36 table_data = fetch_table_data(runs_table_path)
37 all_data_dict['ENA_run'] = table_data
38 # print(all_data_dict)
39 print(yaml.dump(all_data_dict))
40 print('YAML -------------')