Fix outstanding issues with parser and geneset utilites.
geneset_utils.py has a new function get_results() that simplifies a lot of boilerplate code in the parser.
Also, this module adds new top-level fields to genesets duplicates, not_found, count, as well as source_id under the genes field.
Query speedups were achieved by reversing the order of search/retry lists. By preferring gene symbols, we are able to retrieve most genes with a single query, versus using the original ids.
Fixes bugs in the parser that were causing some genes to be missed or queried incorrectly.
Fix outstanding issues with parser and geneset utilites.
geneset_utils.pyhas a new functionget_results()that simplifies a lot of boilerplate code in the parser. Also, this module adds new top-level fields to genesetsduplicates,not_found,count, as well assource_idunder thegenesfield.Query speedups were achieved by reversing the order of search/retry lists. By preferring gene symbols, we are able to retrieve most genes with a single query, versus using the original ids. Fixes bugs in the parser that were causing some genes to be missed or queried incorrectly.