bold_retriever package

Submodules

bold_retriever.bold_retriever module

bold_retriever.bold_retriever.async(seq_record, db, output_filename)

bold_retriever.bold_retriever.cbBody(body, seq_record, output_filename)

bold_retriever.bold_retriever.cbRequest(response, seq_record, output_filename)

bold_retriever.bold_retriever.create_output_file(f)

Containing only column headers of the CSV file.

bold_retriever.bold_retriever.create_parser()

bold_retriever.bold_retriever.generate_jobs(output_filename, fasta_file, db)

Use Twisted.

bold_retriever.bold_retriever.get_args(args)

bold_retriever.bold_retriever.get_started(args)

bold_retriever.bold_retriever.main()

bold_retriever.engine.generate_output_content(all_ids, output_filename, seq_record)

bold_retriever.engine.get(url, payload)

Wrapper function for requests.get so we can mock requests in tests.

Parameters:

• url –
• params – payload

Returns:

response object from requests.get

bold_retriever.engine.get_family_name_for_taxon(tax_id)

Send genus name and get family name from the parentname result form the API.

bold_retriever.engine.get_parentname(taxon)

bold_retriever.engine.get_tax_id_from_web(obj)

Try to get the tax_id from the webpage BIN.

bold_retriever.engine.parse_bold_xml(request, seq_object, id, all_ids, taxon_list)

bold_retriever.engine.process_classification(obj)

bold_retriever.engine.taxon_data(obj)

bold_retriever.engine.taxon_search(obj)

Module contents