Mercurial > repos > ieguinoa > ena_upload

comparison extract_tables.py @ 2:2f7a70c0d3ab draft default tip

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author ieguinoa
date Mon, 21 Feb 2022 14:22:53 +0000
parents 5d59238cd3f4
children
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1:9681a9180730 2:2f7a70c0d3ab
42 studies_table.write('\t'.join([study_alias, action, 'ENA_accession', study['title'], 42 studies_table.write('\t'.join([study_alias, action, 'ENA_accession', study['title'],
43 study['type'], study['abstract'], study['pubmed_id'], 43 study['type'], study['abstract'], study['pubmed_id'],
44 'ENA_submission_data'])) 44 'ENA_submission_data']))
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', 'accession', 'title', 'scientific_name',
47 'taxon_id', 'sample_description', 'collection_date', 47 'taxon_id', 'sample_description', 'collection date',
48 'geographic_location', '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 'submission_date']) + '\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', 'accession', 'title', 'scientific_name',
54 'taxon_id', 'sample_description', 'submission_date']) + '\n') 54 'taxon_id', 'sample_description', 'submission_date']) + '\n')
55 for sample_index, sample in enumerate(study['samples']): 55 for sample_index, sample in enumerate(study['samples']):