Mercurial > repos > iuc > ena_upload
comparison extract_tables.py @ 9:a62c4a11a67d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit 6770d277b4136b4068293c4260022d4ae33b2379
author | iuc |
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date | Thu, 10 Nov 2022 15:18:00 +0000 |
parents | 6f6537780379 |
children | 480d9e9d156b |
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8:d147d6455873 | 9:a62c4a11a67d |
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17 args = parser.parse_args() | 17 args = parser.parse_args() |
18 | 18 |
19 with open(args.studies_json_path, 'r') as studies_json_file: | 19 with open(args.studies_json_path, 'r') as studies_json_file: |
20 studies_dict = json.load(studies_json_file) | 20 studies_dict = json.load(studies_json_file) |
21 studies_table = open(pathlib.Path(args.out_path) / 'studies.tsv', 'w') | 21 studies_table = open(pathlib.Path(args.out_path) / 'studies.tsv', 'w') |
22 studies_table.write('\t'.join(['alias', 'status', 'accession', 'title', 'study_type', | 22 studies_table.write('\t'.join(['alias', 'status', 'title', 'study_type', |
23 'study_abstract', 'pubmed_id', 'submission_date']) + '\n') | 23 'study_abstract', 'pubmed_id']) + '\n') |
24 samples_table = open(pathlib.Path(args.out_path) / 'samples.tsv', 'w') | 24 samples_table = open(pathlib.Path(args.out_path) / 'samples.tsv', 'w') |
25 experiments_table = open(pathlib.Path(args.out_path) / 'experiments.tsv', 'w') | 25 experiments_table = open(pathlib.Path(args.out_path) / 'experiments.tsv', 'w') |
26 experiments_table.write('\t'.join(['alias', 'status', 'accession', 'title', 'study_alias', | 26 experiments_table.write('\t'.join(['alias', 'status', 'title', 'study_alias', |
27 'sample_alias', 'design_description', 'library_name', | 27 'sample_alias', 'design_description', 'library_name', |
28 'library_strategy', 'library_source', 'library_selection', | 28 'library_strategy', 'library_source', 'library_selection', |
29 'library_layout', 'insert_size', | 29 'library_layout', 'insert_size', |
30 'library_construction_protocol', 'platform', 'instrument_model', | 30 'library_construction_protocol', 'platform', 'instrument_model', |
31 'submission_date']) + '\n') | 31 ]) + '\n') |
32 runs_table = open(pathlib.Path(args.out_path) / 'runs.tsv', 'w') | 32 runs_table = open(pathlib.Path(args.out_path) / 'runs.tsv', 'w') |
33 runs_table.write('\t'.join(['alias', 'status', 'accession', 'experiment_alias', 'file_name', | 33 runs_table.write('\t'.join(['alias', 'status', 'experiment_alias', 'file_name', |
34 'file_format', 'file_checksum', 'submission_date']) + '\n') | 34 'file_format']) + '\n') |
35 | 35 |
36 action = args.action | 36 action = args.action |
37 | 37 |
38 dt_oobj = datetime.now(tz=None) | 38 dt_oobj = datetime.now(tz=None) |
39 timestamp = dt_oobj.strftime("%Y%m%d_%H:%M:%S") | 39 timestamp = dt_oobj.strftime("%Y%m%d_%H:%M:%S") |
40 for study_index, study in enumerate(studies_dict): | 40 for study_index, study in enumerate(studies_dict): |
41 study_alias = 'study_' + str(study_index) + '_' + timestamp | 41 study_alias = 'study_' + str(study_index) + '_' + timestamp |
42 studies_table.write('\t'.join([study_alias, action, 'ENA_accession', study['title'], | 42 studies_table.write('\t'.join([study_alias, action, study['title'], |
43 study['type'], study['abstract'], study['pubmed_id'], | 43 study['type'], study['abstract'], study['pubmed_id'], |
44 'ENA_submission_data'])) | 44 ])) |
45 if "geo_location" in study['samples'][0].keys(): # sample belongs to a viral sample | 45 if "geo_location" in study['samples'][0].keys(): # sample belongs to a viral sample |
46 samples_table.write('\t'.join(['alias', 'status', 'accession', 'title', 'scientific_name', | 46 samples_table.write('\t'.join(['alias', 'status', 'title', 'scientific_name', |
47 'taxon_id', 'sample_description', 'collection date', | 47 'taxon_id', 'sample_description', 'collection date', |
48 'geographic location (country and/or sea)', 'host common name', 'host subject id', | 48 'geographic location (country and/or sea)', 'host common name', 'host subject id', |
49 'host health state', 'host sex', 'host scientific name', | 49 'host health state', 'host sex', 'host scientific name', |
50 'collector name', 'collecting institution', 'isolate', | 50 'collector name', 'collecting institution', 'isolate', |
51 'submission_date']) + '\n') | 51 ]) + '\n') |
52 else: | 52 else: |
53 samples_table.write('\t'.join(['alias', 'status', 'accession', 'title', 'scientific_name', | 53 samples_table.write('\t'.join(['alias', 'status', 'title', 'scientific_name', |
54 'taxon_id', 'sample_description', 'submission_date']) + '\n') | 54 'taxon_id', 'sample_description']) + '\n') |
55 for sample_index, sample in enumerate(study['samples']): | 55 for sample_index, sample in enumerate(study['samples']): |
56 sample_alias = 'sample_' + str(sample_index) + '_' + timestamp | 56 sample_alias = 'sample_' + str(sample_index) + '_' + timestamp |
57 if "geo_location" in sample.keys(): # sample belongs to a viral sample | 57 if "geo_location" in sample.keys(): # sample belongs to a viral sample |
58 if sample['collector_name'] == '': | 58 if sample['collector_name'] == '': |
59 sample['collector_name'] = 'unknown' | 59 sample['collector_name'] = 'unknown' |
60 samples_table.write('\t'.join([sample_alias, action, 'ena_accession', sample['title'], | 60 samples_table.write('\t'.join([sample_alias, action, sample['title'], |
61 sample['tax_name'], sample['tax_id'], | 61 sample['tax_name'], sample['tax_id'], |
62 sample['description'], sample['collection_date'], | 62 sample['description'], sample['collection_date'], |
63 sample['geo_location'], sample['host_common_name'], | 63 sample['geo_location'], sample['host_common_name'], |
64 sample['host_subject_id'], sample['host_health_state'], | 64 sample['host_subject_id'], sample['host_health_state'], |
65 sample['host_sex'], sample['host_scientific_name'], | 65 sample['host_sex'], sample['host_scientific_name'], |
66 sample['collector_name'], | 66 sample['collector_name'], |
67 sample['collecting_institution'], sample['isolate'], | 67 sample['collecting_institution'], sample['isolate'], |
68 'ENA_submission_date']) + '\n') | 68 ]) + '\n') |
69 else: | 69 else: |
70 samples_table.write('\t'.join([sample_alias, action, 'ena_accession', sample['title'], | 70 samples_table.write('\t'.join([sample_alias, action, sample['title'], |
71 sample['tax_name'], sample['tax_id'], | 71 sample['tax_name'], sample['tax_id'], |
72 sample['description'], 'ENA_submission_date']) + '\n') | 72 sample['description']]) + '\n') |
73 for exp_index, exp in enumerate(sample['experiments']): | 73 for exp_index, exp in enumerate(sample['experiments']): |
74 exp_alias = 'experiment_' + str(exp_index) + '.' + str(sample_index) + '_' + timestamp | 74 exp_alias = 'experiment_' + str(exp_index) + '.' + str(sample_index) + '_' + timestamp |
75 lib_alias = 'library_' + str(exp_index) + '_' + str(sample_index) | 75 lib_alias = 'library_' + str(exp_index) + '_' + str(sample_index) |
76 experiments_table.write('\t'.join([exp_alias, action, 'accession_ena', exp['title'], | 76 experiments_table.write('\t'.join([exp_alias, action, exp['title'], |
77 study_alias, sample_alias, exp['experiment_design'], | 77 study_alias, sample_alias, exp['experiment_design'], |
78 lib_alias, exp['library_strategy'], | 78 lib_alias, exp['library_strategy'], |
79 exp['library_source'], exp['library_selection'], | 79 exp['library_source'], exp['library_selection'], |
80 exp['library_layout'].lower(), exp['insert_size'], | 80 exp['library_layout'].lower(), exp['insert_size'], |
81 exp['library_construction_protocol'], | 81 exp['library_construction_protocol'], |
82 exp['platform'], exp['instrument_model'], | 82 exp['platform'], exp['instrument_model'], |
83 'submission_date_ENA']) + '\n') | 83 ]) + '\n') |
84 run_index = 0 | 84 run_index = 0 |
85 # exp['runs'] is a list of lists | 85 # exp['runs'] is a list of lists |
86 for (base_run, run_files) in exp['runs']: | 86 for (base_run, run_files) in exp['runs']: |
87 run_index += 1 | 87 run_index += 1 |
88 if base_run != '': | 88 if base_run != '': |
90 else: | 90 else: |
91 # no alias provided, generated a unique one | 91 # no alias provided, generated a unique one |
92 run_alias = '_'.join(['run_' + str(run_index), str(exp_index), | 92 run_alias = '_'.join(['run_' + str(run_index), str(exp_index), |
93 str(sample_index)]) + '_' + timestamp | 93 str(sample_index)]) + '_' + timestamp |
94 for file_entry in run_files: | 94 for file_entry in run_files: |
95 runs_table.write('\t'.join([run_alias, action, 'ena_run_accession', exp_alias, | 95 runs_table.write('\t'.join([run_alias, action, exp_alias, |
96 file_entry, FILE_FORMAT, 'file_checksum', | 96 file_entry, FILE_FORMAT]) + '\n') |
97 'submission_date_ENA']) + '\n') | |
98 | 97 |
99 studies_table.close() | 98 studies_table.close() |
100 samples_table.close() | 99 samples_table.close() |
101 experiments_table.close() | 100 experiments_table.close() |
102 runs_table.close() | 101 runs_table.close() |