DUfddlZddlZddlZddlmZddlmZddl m Z m Z ddl Z ddl mZddlmZdd lmZmZddlZeje jd d e e jd de e jddddee jddedeede jddedde jddde jgd d!"e jd#d$ed%de jd&d'd(d)e jd*d+d,e jd,d-gd!"d.e jd/d0dd!1e jd2d3d4dee jd5d6edde jd7d8d9e jgd:d!"d.e jd;dZdS)?N)api)make_cooler_view)read_viewframe_from_fileread_expected_from_file)partial)cli)sniff_for_header validate_csv cool_path COOL_PATH)metavartypefeatures FEATURES_PATHz--viewz --regionszPath to a BED file which defines which regions of the chromosomes to use. Required if EXPECTED_PATH is provided Note that '--regions' is the deprecated name of the option. Use '--view' instead. )helpdefaultrz --expectedzgPath to the expected table. If provided, outputs OOE pileup. if not provided, outputs regular pileup. z balanced.avg)default_column)rrrcallbackz--flankzSize of flanks.iT)rrr show_defaultz--features-formatzInput features format.auto)rBEDBEDPEF)case_sensitivez--clr-weight-namez$Use balancing weight with this name.weightz-oz--outz$Save output pileup as NPZ/HDF5 file.)rrequiredz --out-formatzType of output.NPZHDF5)rrrrz --store-snipsz0Flag indicating whether snips should be stored. )ris_flagrz-pz--nproczQNumber of processes to split the work between. [default: 1, i.e. no process pool]z--ignore-diagszjThe number of diagonals to ignore. By default, equals the number of diagonals ignored during IC balancing.z --aggregatez+Function for calculating aggregate signal. none)r!meanmedianstdminmaxz-vz --verbosezEnable verbose outputc ftj|}t|}t|\}}|dkrgd}gd}t t jt jt t jt jd}|td|||}nt|dkrtdtd|| }n|d krrgd }gd }t t jt jd }|td||| }nDt|dkrtdtd|| }ntdtj |fd| d|}||}nt||d}|d}n|\}}|g}t|d|||}t j||||||| ||  }| } | | dks| dkr t j}n_| dkr t j}nL| dkr t j}n9| dkr t j}n&| dkr t j}ntd| d||d !}|d"kr3| rt j|||#dSt j||$dS|d%krGt3j|d&}|d'|(| r|d)|(dSdSdS)*a Perform retrieval of the snippets from .cool file. COOL_PATH : The paths to a .cool file with a balanced Hi-C map. Use the '::' syntax to specify a group path in a multicooler file. FEATURES_PATH : the path to a BED or BEDPE-like file that contains features for snipping windows. If BED, then the features are on-diagonal. If BEDPE, then the features can be off-diagonal (but not in trans or between different regions in the view). bedpe)rr r)chrom1start1end1chrom2start2end2N)headerusecolsdtypenameszToo few columns for BEDPEinfer)r2r3r4bed)rr r)chromstartend)r2r3r5r4r)zToo few columns for BEDzoAutomatic detection of features format is not implemented yet. Please provide BED or BEDPE as --features-format#)commentverboseT) check_sortingcis) contact_typeexpected_value_cols verify_view verify_cooler)view_df expected_dfexpected_value_colflankmin_diagclr_weight_namenprocr"r!r#r%r&r$zAggregation mode z3 not supported. Please use mean/median/min/max/std.r)axisnpz)pileupstack)rNhdf5wrN)datarO)coolerCoolerrr lowerstrnpint64dictlen ValueErrorNotImplementedErrorpd read_tablerrrsnippingrNnanmean nanmediannanminnanmaxnanstdsavezh5pyFilecreate_dataset) r rviewexpectedrHfeatures_formatrJout out_format store_snipsrK ignore_diags aggregater>clrcooler_view_dfbufr5 default_cols bedpe_colsdtypeskwargsbed_cols features_dfrErG expected_pathrBrOagg_funcrNh5s Q/var/www/html/software/conda/lib/python3.11/site-packages/cooltools/cli/pileup.pyrNrNsf - " "C%c**N"(++JC'))))) MMM hHhH    =$ FF5zzA~~ !<===*FKKKFF    E ) ) yy ,,,"(CC =\FF5zzA~~ !:;;;(&IIIFF" ?   -LS'LLVLLK | +4DIII!,4) )  +  3     L   -'  E!!II//93F3F: h  < e  9 e  9 e  9 ^ ^ ^ ^   Xe! $ $ $FU""  ) HSu 5 5 5 5 5 5 HS ( ( ( ( ( (     v % % YsC  (000  3   gE  2 2 2 2 2 & % 3 3)pandasr]numpyrWrSr lib.commonrlib.iorrclick functoolsrr utilr r rfcommandargumentrVoptionintChoicerNr~r}rs ))))))FFFFFFFF 00000000   [s;;; O#>>>   Z   1  W\. A A A     !  ...u E E E   /   /      ufoe < < <  ;      *  <   6  777   +3T5Z3Z3   ?><;nZ3Z3Z3r~