diff options
Diffstat (limited to 'scripts')
| -rw-r--r-- | scripts/download_sra_data/download_sra_data.py | 45 |
1 files changed, 28 insertions, 17 deletions
diff --git a/scripts/download_sra_data/download_sra_data.py b/scripts/download_sra_data/download_sra_data.py index 9145a43..e36afb6 100644 --- a/scripts/download_sra_data/download_sra_data.py +++ b/scripts/download_sra_data/download_sra_data.py @@ -8,9 +8,11 @@ import gzip dir_yaml = 'yaml' -date = '2020.06.08' +date = '2020.07.05' -# Query on SRA: 'txid2697049[Organism]' (https://www.ncbi.nlm.nih.gov/sra/?term=txid2697049%5BOrganism%5D) -> Send to -> File -> Full XML -> Create File +# Query on SRA: 'txid2697049[Organism]' (https://www.ncbi.nlm.nih.gov/sra/?term=txid2697049%5BOrganism%5D) +# Query on SRA: 'txid2697049[Organism:noexp] NOT 0[Mbases ' (https://www.ncbi.nlm.nih.gov/sra/?term=txid2697049%5BOrganism:noexp%5D%20NOT%200[Mbases) +# -> Send to -> File -> Full XML -> Create File path_sra_metadata_xml = 'SraExperimentPackage.{}.xml.gz'.format(date) dir_dict_ontology_standardization = '../dict_ontology_standardization/' @@ -70,14 +72,14 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET): accession = RUN.attrib['accession'] run_accession_set.add(accession) #print(accession) - + info_for_yaml_dict['sample']['sample_id'] = accession - SRAFiles = RUN.find('SRAFiles') - if SRAFiles is not None: - url = SRAFiles.find('SRAFile').attrib['url'] - if 'sra-download.ncbi.nlm.nih.gov' in url: - run_accession_to_downloadble_file_url_dict[accession] = url + #SRAFiles = RUN.find('SRAFiles') + #if SRAFiles is not None: + # url = SRAFiles.find('SRAFile').attrib['url'] + # if 'sra-download.ncbi.nlm.nih.gov' in url: + # run_accession_to_downloadble_file_url_dict[accession] = url SAMPLE = EXPERIMENT_PACKAGE.find('SAMPLE') @@ -100,11 +102,19 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET): elif VALUE_text.strip("'") not in ['missing', 'not collected', 'not provided']: missing_value_list.append('\t'.join([accession, 'host_health_status', VALUE_text])) elif TAG_text in ['strain', 'isolate']: - if VALUE_text.lower() not in ['not applicable', 'missing', 'na', 'unknown']: - if 'virus_strain' not in info_for_yaml_dict: - info_for_yaml_dict['virus']['virus_strain'] = VALUE_text + if VALUE_text.lower() not in ['not applicable', 'missing', 'na', 'unknown', 'not provided']: + value_to_insert = VALUE_text + + if value_to_insert.lower() in ['homo sapien']: + value_to_insert = 'Homo sapiens' + + if value_to_insert in term_to_uri_dict: + value_to_insert = term_to_uri_dict[value_to_insert] + + if 'virus_strain' not in info_for_yaml_dict: + info_for_yaml_dict['virus']['virus_strain'] = value_to_insert else: - info_for_yaml_dict['virus']['virus_strain'] += '; ' + VALUE_text + info_for_yaml_dict['virus']['virus_strain'] += '; ' + value_to_insert elif TAG_text in ['isolation_source', 'isolation source host-associated']: if VALUE_text in term_to_uri_dict: info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict[VALUE_text]] @@ -179,17 +189,18 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET): EXPERIMENT = EXPERIMENT_PACKAGE.find('EXPERIMENT') INSTRUMENT_MODEL = [x.text for x in EXPERIMENT.find('PLATFORM').iter('INSTRUMENT_MODEL')][0] + if INSTRUMENT_MODEL.lower() != 'unspecified': if INSTRUMENT_MODEL in term_to_uri_dict: info_for_yaml_dict['technology']['sample_sequencing_technology'] = [term_to_uri_dict[INSTRUMENT_MODEL]] else: missing_value_list.append('\t'.join([accession, 'sample_sequencing_technology', INSTRUMENT_MODEL])) - + #else: + # print(accession, 'Missing INSTRUMENT_MODEL', info_for_yaml_dict) LIBRARY_DESCRIPTOR = EXPERIMENT.find('DESIGN').find('LIBRARY_DESCRIPTOR') if LIBRARY_DESCRIPTOR.text not in ['OTHER']: info_for_yaml_dict['technology']['additional_technology_information'] = 'LIBRARY_STRATEGY: {};'.format(LIBRARY_DESCRIPTOR.find('LIBRARY_STRATEGY').text) - - + SUBMISSION = EXPERIMENT_PACKAGE.find('SUBMISSION') info_for_yaml_dict['submitter']['submitter_sample_id'] = SUBMISSION.attrib['accession'] @@ -197,7 +208,7 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET): info_for_yaml_dict['submitter']['originating_lab'] = SUBMISSION.attrib['lab_name'] STUDY = EXPERIMENT_PACKAGE.find('STUDY') - info_for_yaml_dict['submitter']['publication'] = SUBMISSION.attrib['lab_name'] + info_for_yaml_dict['submitter']['publication'] = STUDY.attrib['alias'] Organization = EXPERIMENT_PACKAGE.find('Organization') @@ -229,4 +240,4 @@ if len(missing_value_list) > 0: path_missing_terms_tsv = 'missing_terms.tsv' print('Written missing terms in {}'.format(path_missing_terms_tsv)) with open(path_missing_terms_tsv, 'w') as fw: - fw.write('\n'.join(missing_value_list)) \ No newline at end of file + fw.write('\n'.join(missing_value_list)) |