o Uݢg@sddZddlmZddlZddlmZmZddlZddl m Z ddl m Z ddlmZgdZdZd:d d Zed;dddZed;d?ddZd;d@ddZed;dAddZed;dBd dZd;dCd"dZdDd$d%ZdEd'd(ZGd)d*d*eZed;dFd+d,Ze dGdHd-d,Ze d;dId.d,ZedJd/d,ZdGdKd0d,Z dLdMd4d5Z dNdOd8d9ZdS)PzBarcode handling functions.) annotationsN)Literaloverload)z odin-5K-v2z visium-v1z visium-v2z visium-v3z visium-v4z visium-v5zomni-v1z omni-hires-v1z omni-pat7-v1z pseudo-xl-v1zthor-v1zthor-v2zthor-v3z thor-XL-v1z thor-XL-v2i whitelist_namestrcCs|tvS)a9Is the barcode a spatial (visium) whitelist? Method returns True if the name is present on a predefined list of spatial barcode whitelist names. Args: whitelist_name: string of the whitelist name Returns: boolean value indicating if the whitelist is from the spatial assay. )SPATIAL_WHITELIST)rrh/oak/stanford/groups/akundaje/marinovg/programs/cellranger-9.0.1/lib/python/cellranger/barcodes/utils.pyis_whitelist_spatial)s r Ffilename str | bytesas_setLiteral[False]return list[bytes]cCdSNrr r rrr load_barcode_tsv8r. Literal[True] set[bytes]cCrrrrrrr r<rboolset[bytes] | list[bytes]cCrrrrrrr r@rcCslt|d}dd|D}Wdn1swYt|}t|t|kr0td||r4|S|S)zLoad barcodes from a tsv file.rbcSsg|] }d|vr|qS)#)strip).0xrrr Gsz$load_barcode_tsv..Nz'Duplicates found in barcode whitelist: )cr_ioopen_maybe_gzipsetlen Exception)r r Zbc_filebarcodesZ barcode_setrrr rDs None translationcCrrrr r'rrr get_barcode_whitelist_pathNrr)cCrrrr(rrr r)Rr str | NonecCsl|durdStj|r|Stj}|rtj|d}tj||d}tj|r+|Stj||d}|S)Nr'.txt.gz.txt)ospathexists cr_constantsBARCODE_WHITELIST_PATHjoin)r r'Zrootdirgztxtrrr r)Vs   list[str]cCs`ttj}d}g}|D]!}tjtj|}||r-|ddkr-tj|r-| |q |S)zFunction to return the set of all whitelist names included in the product. Uses some heuristics to search through folders in this directory. Returns: A list of strings, one per filename r,r+ coordinatesr) r-listdirr0r1r.r2endswithcountisfileappend)Z basenamesZallowed_suffixesZ all_filesnameZ full_namerrr get_all_whitelist_filenamesis   r> filenamescCs|d}ddd|DS)N,cSsg|]}t|qSr)r))rprrr rsz/get_barcode_whitelist_paths..)splitr2)r?pathsrrr get_barcode_whitelist_pathss rDc@seZdZdZdS)WhitelistNotFoundz+Raised when a named whitelist is not found.N)__name__ __module__ __qualname____doc__rrrr rEsrEcCrrrrrrr load_barcode_whitelistrrJcCrrrr r r'rrr rJcCrrrrKrrr rJrLcCrrrrKrrr rJrLcCs:t||}|dur dStj|std|t||S)Nz"Unable to find barcode whitelist: )r)r-r.r;rEr)r r r'r.rrr rJs   r=r.dict[str, str] | NonecCs|dur |dur dS|dur|durJ|dur4d}dD]}tjtj||}tj|r2|}nqn|}|durrDr$rErJrXrerrrr sR             $