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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 pathlib
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21
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4 from datetime import datetime
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5
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25
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6 FILE_FORMAT = 'fastq'
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7
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4
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8 parser = argparse.ArgumentParser()
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25
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9 parser.add_argument('--studies', dest='studies_json_path', required=True)
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10 parser.add_argument('--out_dir', dest='out_path', required=True)
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11 parser.add_argument('--action', dest='action', required=True)
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4
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12 args = parser.parse_args()
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13
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25
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14 with open(args.studies_json_path, 'r') as studies_json_file:
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4
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15 studies_dict = json.load(studies_json_file)
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16 studies_table = open(pathlib.Path(args.out_path) / 'studies.tsv', 'w')
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25
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17 studies_table.write('\t'.join(['alias', 'status', 'accession', 'title', 'study_type',
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18 'study_abstract', 'pubmed_id', 'submission_date']) + '\n')
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4
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19 samples_table = open(pathlib.Path(args.out_path) / 'samples.tsv', 'w')
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25
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20 experiments_table = open(pathlib.Path(args.out_path) / 'experiments.tsv', 'w')
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21 experiments_table.write('\t'.join(['alias', 'status', 'accession', 'title', 'study_alias',
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22 'sample_alias', 'design_description', 'library_name',
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23 'library_strategy', 'library_source', 'library_selection',
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24 'library_layout', 'insert_size',
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25 'library_construction_protocol', 'platform', 'instrument_model',
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26 'submission_date']) + '\n')
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27 runs_table = open(pathlib.Path(args.out_path) / 'runs.tsv', 'w')
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28 runs_table.write('\t'.join(['alias', 'status', 'accession', 'experiment_alias', 'file_name',
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29 'file_format', 'file_checksum', 'submission_date']) + '\n')
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4
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30
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25
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31 action = args.action
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21
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32
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33 dt_oobj = datetime.now(tz=None)
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34 timestamp = dt_oobj.strftime("%Y%m%d_%H:%M:%S")
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4
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35 for study_index, study in enumerate(studies_dict):
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25
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36 study_alias = 'study_' + str(study_index) + '_' + timestamp
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37 studies_table.write('\t'.join([study_alias, action, 'ENA_accession', study['title'],
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38 study['type'], study['abstract'], study['pubmed_id'],
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39 'ENA_submission_data']))
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40 if "geo_location" in study['samples'][0].keys(): # sample belongs to a viral sample
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41 samples_table.write('\t'.join(['alias', 'status', 'accession', 'title', 'scientific_name',
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42 'taxon_id', 'sample_description', 'collection_date',
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43 'geographic_location', 'host_common_name', 'host_subject_id',
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44 'host_health_state', 'host_sex', 'host_scientific_name',
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45 'collector_name', 'collecting_institution', 'isolate',
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46 'submission_date']) + '\n')
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15
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47 else:
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25
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48 samples_table.write('\t'.join(['alias', 'status', 'accession', 'title', 'scientific_name',
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49 'taxon_id', 'sample_description', 'submission_date']) + '\n')
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50 for sample_index, sample in enumerate(study['samples']):
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51 sample_alias = 'sample_' + str(sample_index) + '_' + timestamp
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52 if "geo_location" in sample.keys(): # sample belongs to a viral sample
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15
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53 if sample['collector_name'] == '':
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54 sample['collector_name'] = 'unknown'
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25
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55 samples_table.write('\t'.join([sample_alias, action, 'ena_accession', sample['title'],
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56 sample['tax_name'], sample['tax_id'],
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57 sample['description'], sample['collection_date'],
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58 sample['geo_location'], sample['host_common_name'],
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59 sample['host_subject_id'], sample['host_health_state'],
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60 sample['host_sex'], sample['host_scientific_name'],
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61 sample['collector_name'],
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62 sample['collecting_institution'], sample['isolate'],
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63 'ENA_submission_date']) + '\n')
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15
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64 else:
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25
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65 samples_table.write('\t'.join([sample_alias, action, 'ena_accession', sample['title'],
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66 sample['tax_name'], sample['tax_id'],
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67 sample['description'], 'ENA_submission_date']) + '\n')
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68 for exp_index, exp in enumerate(sample['experiments']):
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69 exp_alias = 'experiment_' + str(exp_index) + '.' + str(sample_index) + '_' + timestamp
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70 lib_alias = 'library_' + str(exp_index) + '_' + str(sample_index)
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71 experiments_table.write('\t'.join([exp_alias, action, 'accession_ena', exp['title'],
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72 study_alias, sample_alias, exp['experiment_design'],
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73 lib_alias, exp['library_strategy'],
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74 exp['library_source'], exp['library_selection'],
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75 exp['library_layout'].lower(), exp['insert_size'],
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76 exp['library_construction_protocol'],
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77 exp['platform'], exp['instrument_model'],
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78 'submission_date_ENA']) + '\n')
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4
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79 run_index = 0
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80 # exp['runs'] is a list of lists
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81 for run in exp['runs']:
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82 run_index += 1
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25
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83 run_alias = '.'.join(['run_' + str(run_index), str(exp_index), str(sample_index)]) \
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84 + '_' + timestamp
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4
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85 for file_entry in run:
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25
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86 runs_table.write('\t'.join([run_alias, action, 'ena_run_accession', exp_alias,
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87 file_entry, FILE_FORMAT, 'file_checksum',
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88 'submission_date_ENA']) + '\n')
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4
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89
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90 studies_table.close()
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91 samples_table.close()
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92 experiments_table.close()
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93 runs_table.close()
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