Mercurial > repos > iuc > ena_upload
diff extract_tables.py @ 10:480d9e9d156b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit dccd4c0668ec8ce1b1c8fd9cef4dcf3a99dc78b3
author | iuc |
---|---|
date | Fri, 27 Oct 2023 19:44:40 +0000 |
parents | a62c4a11a67d |
children |
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--- a/extract_tables.py Thu Nov 10 15:18:00 2022 +0000 +++ b/extract_tables.py Fri Oct 27 19:44:40 2023 +0000 @@ -40,21 +40,20 @@ for study_index, study in enumerate(studies_dict): study_alias = 'study_' + str(study_index) + '_' + timestamp studies_table.write('\t'.join([study_alias, action, study['title'], - study['type'], study['abstract'], study['pubmed_id'], - ])) - if "geo_location" in study['samples'][0].keys(): # sample belongs to a viral sample + study['type'], study['abstract'], study['pubmed_id']])) + if "host_subject_id" in study['samples'][0].keys(): # sample belongs to a viral sample samples_table.write('\t'.join(['alias', 'status', 'title', 'scientific_name', 'taxon_id', 'sample_description', 'collection date', 'geographic location (country and/or sea)', 'host common name', 'host subject id', 'host health state', 'host sex', 'host scientific name', - 'collector name', 'collecting institution', 'isolate', - ]) + '\n') + 'collector name', 'collecting institution', 'isolate']) + '\n') else: samples_table.write('\t'.join(['alias', 'status', 'title', 'scientific_name', - 'taxon_id', 'sample_description']) + '\n') + 'taxon_id', 'sample_description', 'collection date', + 'geographic location (country and/or sea)']) + '\n') for sample_index, sample in enumerate(study['samples']): sample_alias = 'sample_' + str(sample_index) + '_' + timestamp - if "geo_location" in sample.keys(): # sample belongs to a viral sample + if "host_subject_id" in sample.keys(): # sample belongs to a viral sample if sample['collector_name'] == '': sample['collector_name'] = 'unknown' samples_table.write('\t'.join([sample_alias, action, sample['title'], @@ -64,12 +63,13 @@ sample['host_subject_id'], sample['host_health_state'], sample['host_sex'], sample['host_scientific_name'], sample['collector_name'], - sample['collecting_institution'], sample['isolate'], + sample['collecting_institution'], sample['isolate'] ]) + '\n') else: samples_table.write('\t'.join([sample_alias, action, sample['title'], sample['tax_name'], sample['tax_id'], - sample['description']]) + '\n') + sample['description'], sample['collection_date'], + sample['geo_location']]) + '\n') for exp_index, exp in enumerate(sample['experiments']): exp_alias = 'experiment_' + str(exp_index) + '.' + str(sample_index) + '_' + timestamp lib_alias = 'library_' + str(exp_index) + '_' + str(sample_index) @@ -79,8 +79,7 @@ exp['library_source'], exp['library_selection'], exp['library_layout'].lower(), exp['insert_size'], exp['library_construction_protocol'], - exp['platform'], exp['instrument_model'], - ]) + '\n') + exp['platform'], exp['instrument_model']]) + '\n') run_index = 0 # exp['runs'] is a list of lists for (base_run, run_files) in exp['runs']: