o Uݢg @sTdZddlmZddlZddlmZddlmZGdddeZ Gdd d e Z dS) zRA file to read and ingest cell_barcodes.json files produced by PARSE_MULTI_CONFIG.) annotationsN)load_barcode_whitelist)-get_whitelist_name_from_chemistry_descriptionc@seZdZdZdS)InvalidCellBarcodez&Barcode is not from a given whitelist.N)__name__ __module__ __qualname____doc__r r g/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/python/cellranger/cell_barcodes.pyrsrcs*eZdZdZfddZdddZZS) CellBarcodeszKPython equivalent of file produced by Rust code, list of barcodes as bytes.csVtt|}t|D] }||qWddS1s$wYdS)aLoad a JSON file with a list of barcodes. e.g. like .. code-block:: python to_keep = [ "AACAAAGAGCAACCAG-1", "AACGAAAGTGACCGAA-1", "AAGCGAGCAGTTGAAA-1", "AAGCGTTTCCCGTTCA-1", "AAGTGAACAAGATGGC-1", "AATCACGTCGTAACTG-1", "AATGGAAGTTAAGCAA-1", "AATGGAAGTTCCTTGC-1", "AATTCCTAGCCATTTG-1" ] Args: json_file_name: json path to load N)super__init__openjsonloadappendencode)selfZjson_file_namefbc __class__r r rs  "zCellBarcodes.__init__chemistry_description str | NonecCsl|dur0t|}|dur2t|ddd}|D]}|dd}||vr/td|d|qdSdSdS) aqGiven a chemistry description (which corresponds to a "description" in the chemistry_defs.json. try to load the whitelist and verify that everything in this list is on that whitelist. Args: chemistry_description: string that corresponds to a "description" in the chemistry_defs.json Returns: None or Exception NnameT)Zas_set-rz Barcode: z is invalid for the chemistry )rrsplitrdecode)rrZwhitelist_name whitelistbarcodeZ stripped_bcr r r verify_bcs_match_whitelist0s z'CellBarcodes.verify_bcs_match_whitelist)rr)rrrr rr! __classcell__r r rr r s r ) r __future__rrZcellranger.barcodes.utilsrcellranger.chemistryr Exceptionrlistr r r r r s