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