o Nrf @s ddlZddlmmZddlZddlZddlZ ddl m Z m Z m Z ddlmZdZdZeeZiZddd ed<d d d ed <d d d ed <ddd ed<iZddd ed<ddd ed<ddZddZd"ddZddZ   d#ddZidfddZd d!ZdS)$N)get_quadtree_depth abs2genomic natsorted)ThreadPoolExecutoriZMeanmean)namevalueZMinminZMaxmaxzStandard DeviationstdzMin-MaxminMaxZWhiskerwhiskercCs&ddtt|tdDdddS)NcSsg|]}d|qS)).0xrr]/var/www/html/software/conda/envs/catlas/lib/python3.10/site-packages/clodius/tiles/bigwig.py z(get_zoom_resolutions..r)ranger TILE_SIZE) chromsizesrrrget_zoom_resolutionss&rcCs(t|}t|}t||}|S)zj TODO: replace this with negspy Also, return NaNs from any missing chromosomes in bbi.fetch )bbirrkeyspdSeries)bwpathrZ chromosomes chrom_seriesrrrget_chromsizess  r"c Cs|durt|}g}|D] \}}||t|gg7}qn |}dd|D}t|t}dgt|gtd|t||ttd}|S)a* Get the tileset info for a bigWig file Parameters ---------- bwpath: string The path to the bigwig file from which to retrieve data chromsizes: [[chrom, size],...] A list of chromosome sizes associated with this tileset. Typically passed in to specify in what order data from the bigwig should be returned. Returns ------- tileset_info: {'min_pos': [], 'max_pos': [], 'tile_size': 1024, 'max_zoom': 7 } NcSg|]}t|dqSrintrcrrrrHz tileset_info..rr)Zmin_posZmax_pos max_width tile_sizemax_zoomraggregation_modes range_modes)r"itemsr&rrsumr-r.)r rZchromsizes_listchromsizer, tileset_inforrrr3+s&   r3cCs|\}}}}}}}}tt|||} d} |dkrd} |dkr#d} | dkr.t| | fnt| } z|j|} |j|} || ||g}| tjd}|dkrstj|it |dd| ddd f<tj|it |d d| dddf<n]|dkrtj|it |dd| ddd f<tj|it |d d| dddf<tj|it |d d| dddf<tj|it |d d| ddd f<ntj|it ||d| dd<|| kr| |d kr| dd} W| SW| SW| St ytj| dd<Y| St y tj| dd<Y| Sw)Nrrrrr)Zbinsmissingr )summaryrr rr r) r&npceilZzerosindexvaluesnanrfetchdict IndexErrorKeyError)ar binsizeraggregation_mode range_modeZcidstartendZn_binsZn_dimrr1Zclenargskwargsrrr fetch_dataYsH     $&$$$&    rHc sdurtt}||tt||}tdd} t| tfdd|D} Wdn1s;wYt| S)N) max_workerscs&g|]}tgt|qSr)tuplelistr'rBrAr rrCrrrs z#get_bigwig_tile..) r"rrLrrmaprHr7Z concatenate) r zoom_level start_posend_posrrBrC resolutionsZcids_starts_endseZarraysrrMrget_bigwig_tiles    rTc Csng}|D]}|ddd}|dd}|d}ttt|dd} t|dkr0|dnd} | tvr8| nd} | tvr@| nd} tdd |D} |rcd d |D}d d |D}tj ||d }nd}d | vrm| d }||vrv||}nd}| d}| d}|durt |}t |t }t d||}||}||}t |||||| | d}t|}|||fg7}q|S)a  Generate tiles from a bigwig file. Parameters ---------- tileset: tilesets.models.Tileset object The tileset that the tile ids should be retrieved from tile_ids: [str,...] A list of tile_ids (e.g. xyx.0.0) identifying the tiles to be retrieved chromsizes_map: {uid: []} A set of chromsizes listings corresponding to the parameters of the tile_ids. To be used if a chromsizes id is passed in with the tile id with the `|cos:id` tag in the tile id chromsizes: [[chrom, size],...] A 2d array containing chromosome names and sizes. Overrides the chromsizes in chromsizes_map Returns ------- tile_list: [(tile_id, tile_data),...] A list of tile_id, tile_data tuples |rNr.r6rcSsg|]}|dqS):)split)rorrrrsztiles..cSsg|]}|dqS)rrr'rrrrrcSr#r$r%r'rrrrr))r9cosr)rBrC)rXrLrNr&lenr-r.r=rrr"rrrThgfoZformat_dense_tile)r Ztile_idsZchromsizes_maprZgenerated_tilesZtile_idZtile_option_partsZtile_no_optionsZ tile_id_partsZ tile_position return_valuerBrCZ tile_optionsZ chromnamesZ chromlengthsZchromsizes_to_useZ chromsizes_idrOZtile_pos max_depthr+rPrQZdenseZ tile_valuerrrtilessP    r_c Csdzt|}g}|D] \}}|||gq |WSty1}z t|td|d}~ww)a, Get a list of chromosome sizes from this [presumably] bigwig file. Parameters: ----------- filename: string The filename of the bigwig file Returns ------- chromsizes: [(name:string, size:int), ...] An ordered list of chromosome names and sizes z-Error loading chromsizes from bigwig file: {}N)r"r/append Exceptionloggererrorformat)filenamer!datar1r2exrrrrs r)N)NrN)rZclodius.tiles.formatr_rdr\loggingnumpyr7Zpandasrutilsrrrconcurrent.futuresrZ MAX_THREADSr getLogger__name__rbr-r.rr"r3rHrTrrrrrs8   .5 ! N