diff options
Diffstat (limited to 'scripts/create_sra_metadata/create_sra_metadata.py')
| -rw-r--r-- | scripts/create_sra_metadata/create_sra_metadata.py | 15 |
1 files changed, 9 insertions, 6 deletions
diff --git a/scripts/create_sra_metadata/create_sra_metadata.py b/scripts/create_sra_metadata/create_sra_metadata.py index f5dc0c8..89624fd 100644 --- a/scripts/create_sra_metadata/create_sra_metadata.py +++ b/scripts/create_sra_metadata/create_sra_metadata.py @@ -228,7 +228,7 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET): taxon_id = SAMPLE.find('SAMPLE_NAME').find('TAXON_ID').text - info_for_yaml_dict['virus']['virus_species'] = "http://purl.obolibrary.org/obo/NCBITaxon_"+taxon_id + info_for_yaml_dict['virus']['virus_species'] = "http://purl.obolibrary.org/obo/NCBITaxon_" + taxon_id # This script download and prepare data and metadata for samples that will be mapepd againg a referenceT info_for_yaml_dict['technology']['assembly_method'] = 'http://purl.obolibrary.org/obo/GENEPIO_0002028' @@ -244,22 +244,25 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET): #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']: + 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'] + if SUBMISSION.attrib['accession']: + info_for_yaml_dict['submitter']['submitter_sample_id'] = SUBMISSION.attrib['accession'] - if SUBMISSION.attrib['lab_name'].lower() not in ['na']: + if SUBMISSION.attrib['lab_name'].lower() not in ['', 'na']: info_for_yaml_dict['submitter']['originating_lab'] = SUBMISSION.attrib['lab_name'] STUDY = EXPERIMENT_PACKAGE.find('STUDY') - info_for_yaml_dict['submitter']['publication'] = STUDY.attrib['alias'] + if STUDY.attrib['alias']: + info_for_yaml_dict['submitter']['publication'] = STUDY.attrib['alias'] Organization = EXPERIMENT_PACKAGE.find('Organization') Organization_Name = Organization.find('Name') - info_for_yaml_dict['submitter']['authors'] = [Organization_Name.text] + if Organization_Name.text: + info_for_yaml_dict['submitter']['authors'] = [Organization_Name.text] Organization_Contact = Organization.find('Contact') if Organization_Contact is not None: |