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4
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1 import argparse
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2 import json
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3 import os
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4 import pathlib
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5
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6 parser = argparse.ArgumentParser()
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7 parser.add_argument('--studies',dest='studies_json_path', required=True)
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8 parser.add_argument('--out_dir',dest='out_path', required=True)
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9 args = parser.parse_args()
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10
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11
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12 with open(args.studies_json_path,'r') as studies_json_file:
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13 studies_dict = json.load(studies_json_file)
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14
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15 studies_table = open(pathlib.Path(args.out_path) / 'studies.tsv', 'w')
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16 studies_table.write('\t'.join(['alias','status','accession','title','study_type','study_abstract','pubmed_id','submission_date']) + '\n')
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17
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18 samples_table = open(pathlib.Path(args.out_path) / 'samples.tsv', 'w')
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19 samples_table.write('\t'.join(['alias','status','accession','title','scientific_name','taxon_id','sample_description','submission_date']) + '\n')
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20
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21 experiments_table = open(pathlib.Path(args.out_path) / 'experiments.tsv', 'w')
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22 experiments_table.write('\t'.join(['alias','status','accession','title','study_alias','sample_alias','design_description','library_name','library_strategy','library_source','library_selection','library_layout','insert_size','library_construction_protocol','platform','instrument_model','submission_date'])+ '\n')
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23
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24 runs_table = open(pathlib.Path(args.out_path) / 'runs.tsv', 'w')
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25 runs_table.write('\t'.join(['alias','status','accession','experiment_alias','file_name','file_format','file_checksum','submission_date'])+ '\n')
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26
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27 action = 'add'
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28 for study_index, study in enumerate(studies_dict):
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29 study_alias = 'study_'+str(study_index)
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30 studies_table.write('\t'.join([study_alias,action,'ENA_accession',study['title'], study['type'],study['abstract'],study['pubmed_id'],'ENA_submission_data']))
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31 for sample_index,sample in enumerate(study['samples']):
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32 sample_alias = 'sample_'+str(sample_index)
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33 samples_table.write('\t'.join([sample_alias,action,'ena_accession',sample['title'],sample['tax_name'], sample['tax_id'],sample['description'],'ENA_submission_date'])+ '\n')
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34 for exp_index,exp in enumerate(sample['experiments']):
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35 exp_alias = 'experiment_'+str(exp_index)+'_'+str(sample_index)
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36 lib_alias = 'library_'+str(exp_index)+'_'+str(sample_index)
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37 experiments_table.write('\t'.join([exp_alias,action,'accession_ena',exp['title'],study_alias,sample_alias,exp['experiment_design'],lib_alias,exp['library_strategy'],exp['library_source'],exp['library_selection'],exp['library_layout'],exp['insert_size'],exp['library_construction_protocol'],exp['platform'],exp['instrument_model'],'submission_date_ENA']) + '\n')
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38 run_index = 0
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39 # exp['runs'] is a list of lists
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40 for run in exp['runs']:
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41 run_index += 1
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42 run_alias = '_'.join(['run',str(exp_index),str(sample_index),str(run_index)])
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43 for file_entry in run:
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44 file_format = 'fastq.gz' if os.path.splitext(file_entry)[-1] == '.gz' else 'fastq.bz2'
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45 runs_table.write('\t'.join([run_alias,action,'ena_run_accession',exp_alias,file_entry,file_format,'file_checksum','submission_date_ENA']) + '\n')
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46
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47 studies_table.close()
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48 samples_table.close()
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49 experiments_table.close()
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50 runs_table.close()
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