tfR8ddlZddlZddlmcmZddlmcmZ ddl Z ddl Z ddl ZddlZddlZej$eZiaiZddded<ddded<ddded<ddded<dZd Zd Z dd Zd Zd ZdZ ddZdZdZ dZ!dZ"dZ#dZ$dZdZ%y)NICEweightnamevalueKRVCVC_SQRTc tj||kDddz }||}|||z }|j ||||fS#t$r|jdcYSwxYw)zGet bin ID from absolute coordinates. Args: c (Cooler): Cooler instance of a .cool file. abs_pos (int): Absolute coordinate to be translated. Returns: int: Bin number. rnbins)np flatnonzero IndexErrorinfooffset)cabs_poschromschrom_cum_lengths chrom_sizeschr_idchromrel_poss ^/var/www/html/software/conda/envs/higlass/lib/python3.12/site-packages/clodius/tiles/cooler.pyabs_coord_2_binrsz 1G ; (list(string), dict, np.array(int)) r) chromnamesdict chromsizesrr_cumsumvalues)r chrom_namesrrs r"get_chromosome_names_cumul_lengthsr&/sP,,Kq||$Ka1<<+>+>!??@  %6 66c0tj|}t|\}} } t|||| | } t|||| | } t|||| | } t|||| | }|j dd}| |j dk\s| |j dk\rQd\} } } }t jgdt jgggd t jgggd ffSt| |j ddz } t||j ddz }|| | dz| |dzf} gd }|d k(rd |jvs|d k(r|jd n|d vr|j||jd|}tj||}| |d|dz|d<| |d|dz|d<|| | dz}|| |dz}| |d|dz|d<| |d|dz|d<| |d|dz|d<| |d|dz|d<|d k(rd |jvs|d k(r|d|dz|dz|d<|gd||ffS|d vr5|d||dzz ||dzz |d<|||d <|||d <|gd||ffS|gd d!fS)"a>Get balanced pixel data. Args: f: h5py.File An HDF5 Group that contains the cooler for this resolution start_pos_1 (int): Test. end_pos_1 (int): Test. start_pos_2 (int): Test. end_pos_2 (int): Test. Returns: DataFrame: Annotated cooler pixels. TF) as_pixelsbalancerr )rrrr) genome_start1 genome_start2balanced)columns) genome_start genome_endr)rstartenddefaultr)rr r ) convert_enumchrom1start1r+chrom2start2r,rr1r/r2r0countweight1weight2r-12)r+r,r9)NN) coolerCoolerr&rmatrixshapepd DataFrameminbinsappendannotate)f start_pos_1 end_pos_1 start_pos_2 end_pos_2 transform resolutionrrrri0i1j0j1r@pixelscolsrEbins1bins2s rget_datarWAsS.  aA/QRS/T,V[+ K1BK PB Iv/@+ NB K1BK PB Iv/@+ NB XXeX 4F V\\!_fll1o 5$BB LL!O P bbQR bbQR   V\\!_q( ) V\\!_q( ) BaKb1f, -F %DY8qvvx#7Ir?r&intstr TILE_SIZEranger$) file_pathrHr_rrrr total_lengthbin_sizer`rbi f_for_zoomrs r_get_info_multi_v1rrs 9c "' a77;;z*   KK (CD D MM!C& !3UVW3X0/,R01 77:&qX'--j9:y(1=8  x PA3q66*J:%05'I 8$z!,04#@ 4 z!,04#@ 4 J&1:Y(O 9% PSz$l3 ""+$++-  A' R KS' R KsC>E )E  Ecttj||tzdzDcgc] }|d|zz c}Scc}w)Nr r\)rlhgutget_quadtree_depthrk)r!base_resxs rget_zoom_resolutionsrxsJt..z8i;OPSTTU   16  s>ctjj|d}t||}t dj d|Dy)ze Print comma-separated list of zoom resolutions for a given genome and base resolution. T) all_names,c32K|]}t|yw)N)rj).0ress r z)print_zoom_resolutions..s33s83sN)r>utilread_chromsizesrxprintjoin)chromsizes_filervr! resolutionss rprint_zoom_resolutionsrs@ ,,_,MJ&z8r?r&sumr$rWrlastyperir nan_to_numzerosfloat32isnanarraynanravel)&hdf_for_resolutionrNx_posy_postransform_typex_widthy_width BINS_PER_TILE tile_sizer6end1r8end2rrrrrndatarUrVdata_by_tileposx_offsety_offsetdfbinsizejrpvout sub_bins1 sub_bins2 nan_bins1 nan_bins2bibjbend1bend2s& r make_tilesrs BM]*I Y F GOy (D Y F GOy (D  ()A/QRS/T,V[+{))+,L% q qT>E5"O!W%HPa)G PHh&)3FH$q(I5Dh&)3FH$q(I5Dd?+v56BB'$./BB'612BB'$./B G_%,,v5'AII#NA_%,,v5'AII#NARMM"Z."7"78MM"W+"4"45((:RZZ8CC1I U%6!%"76"AB !%"76"AB %i&?$&FG %i&?$&FG &bhhy/B&CD %bhhy/B&CD  077&@WLTT!077&@WLTT XXeL#d)S_MNQWW&+ XXeL#d)S_MNQWW&+ eqj)eqj)VVArE VVBE "AuH "E1H EHIIKOUX-ux/?@ AOG PHPT r'c tjt}|D]U}|jd}t t t |dd}|d}t|}|||fj|W|S)ap Place these tiles into separate lists according to their zoom level and transform type Parameters ---------- tile_ids: [str,...] A list of tile_ids (e.g. xyx.0.0.1) identifying the tiles to be retrieved Returns ------- tile_lists: {(zoomLevel, transformType): [tile_id, tile_id]} A dictionary of tile ids .r r) col defaultdictsetsplitlistmapriget_transform_typeadd)tile_ids tile_id_liststile_id tile_id_parts tile_position zoom_leveltransform_methods r%bin_tiles_by_zoom_level_and_transformrs OOC(MC c* SmAa&89: "1% -g6z#34599'BC r'cV|jd}t|dkDr|d}|Sd}|S)z Get the transform type specified in the tile id. Parameters ---------- cooler_tile_id: str A tile id for a 2D tile (cooler) Returns ------- transform_type: str The transform type requested for this tile rrr3)rlen)rrrs rrrs@MM#&M =A(+ % r'ct}|d}d|vr|jdd|vr|jdd|vr|jdd|vr|jd|S)a  Get the available resolutions from a single cooler file. Parameters ---------- cooler: h5py File A cooler file containing binned 2D data Returns ------- transforms: dict A list of transforms available for this dataset rErrr r )rr)r>rbrqs rget_available_transformsrsjJJ:x  zt ztJy! r'c tj|d}d|vrydttt t t |dji}||gt|<i}|dD]}t|dt|||<!tj|j}|Dcgc] }t| c}|d<t |djd}t t|d|dd}||g|d<ddg|d <t!j"|d|}|j$j'D cgc]} | dt | dgc} |d <d |j(vr|j(d d k(rd |d<||fSt+|}t!j"|d}|j$j'D cgc]} | dt | dgc} |d <|d D cgc] } t | c} |d <|dD cgc] } t | c} |d<t |d|d<t |d|d<d|vrt |d|d<d|j(vr|j(dsd |d<d |j(vr|j(d d k(rd |d<||gt|<||fScc}wcc} wcc} wcc} wcc} w)zJ Create the file handle and tileset info for a cooler tileset rYrrbrrlengthr^r r]r!z storage-modesquarefalse mirror_tilesrZr_r` symmetric)rcrdtuplesortedrrirkeysmatsrrjr intersectionr$transform_descriptionsrr>r?r!itemsrrr) filepathrHr#available_transforms_per_resolutionrNall_available_transformst genome_lengthrrwms r make_matsrs (C AuVCT!M:J:O:O:Q5R,S%TUVTX /1+}- J>V- Z1? / ;  $'#3#3 0 7 7 9$  0H *+ "1 % \ !M*//1215 C- 0 ((J#*D . d7N+"(+ MM!C& !9:9K9K9MNAqtS1Y/N\+/ ?;a3q6;Y+/ ?;a3q6;YtJ/0Z[ 12[ 4 !%d<&8!9D  !&&  )<#*D QVV #~(>((J#*D TX d7NK OO;;s2J? KK ;KKcJ|tvr t|dSt|\}}|S)z Get the tileset info for a cooler file Parameters: ----------- filepath: str The location of the cooler file r )rr)rrHrs r tileset_infors.4H~a  h' D r'c|jd}|d}|dd}t|}dj|g|z|gz}|S)a Add a transform type to a cooler tile id if it's not already present. Parameters ---------- tile_id: str A tile id (e.g. xyz.0.1.0) Returns ------- new_tile_id: str A formatted tile id, potentially with an added transform_type rrr r)rrr)rr tileset_uuidrr new_tile_ids radd_transform_typer&sUMM#&M #L!!A&M'0N((L>M9^s"$L&(1 3:#K0 % & %X|? ?O @ r'cd}|tvr t|t|}t|j}t t j |Dcgc]}tj|c}}g}|D]=}t|djdd} |djdd} t|d} |d|d} dvrMtdD cgc] } t| c} d}| t|kDr|| }| dt|}n%| dkDr| t| }d d | zz |z }|Dcgc]-}|jdd d Dcgc] }t|c}/}}}t tfd |}t tfd |}t|dk(rCt!|Dcgc]}|d c}}t#|Dcgc]}|d c}}t!|Dcgc]}|d c}}t#|Dcgc]}|d c}}t%||||| ||z dz||z dz}|j'Dcgc]N\}}dj)t+t| g| gzt |z| gzt-j.|fP}}}||z }@|Scc}wcc} wcc}wcc}}wcc}wcc}wcc}wcc}wcc}}w)a Generate tiles from a cooler file. Parameters ---------- tileset: tilesets.models.Tileset object The tileset that the tile ids should be retrieved from tile_ids: [str,...] A list of tile_ids (e.g. xyx.0.0.1) identifying the tiles to be retrieved Returns ------- generated_tiles: [(tile_id, tile_data),...] A list of tile_id, tile_data tuples r rrr rT)reverser_r`r\rc&|ddddzkS)Nrr^r rwrs rz generate_tiles..QqTL$;A$>$BBr'c&|ddddzkS)Nr r^rrs rrz generate_tiles..rr')rrrr$ritchainrtpartition_by_adjacent_tilesrirrrrrjfilterrDmaxrrrrhgfoformat_dense_tile)rrrtileset_file_and_infotile_ids_by_zoom_and_transformrpartitioned_tile_idsr tile_groupr tileset_idr tileset_filerYsorted_resolutionsrNrrwtile_positionsminxmaxxminymaxytile_data_by_positionposition tile_datarrs @rrrUs1Mt( N%J& fh#  8003 O*C! A,,S1!45 ]((-a0 +JqM:,Q/ ,Q/ L (!'!-m!<=AQ=t" C 233+J7J!-m! &{3a:oEVJGQR!1773<!+<=a3q6=RR BN S  BN S  ~ ! # .1QAaD12.1QAaD12.1QAaD12.1QAaD12 *      4K!O 4K!O! (*?)D)D)F  &9# |3d8nDGWW &&y1      5 GC!J ]$>>R2111  sCJ< K K "K4K  K ! K = K  K AK%K )r3N)r3r r )& collectionsrr>clodius.tiles.formatrformatrclodius.tiles.utilsutilsrtrc itertoolsrnumpyrpandasrBlogging getLogger__name__rgrrrkrr&rWrrrxrrrrrrrrrrr'rrs ##""    8 $ ,1H#Ex (,t<t(,t<t-6$Ky!  :,70`SF3l5  Rj<,8@F$0.jr'