DUfddlZddlmZddlmZddlmZddlZddlmZej ej dd e d ej d d d de ej ddde e ddej ddde dej dddejddej ddd ej d!d"d ej d#d$ed%dej d&d'e d(dej d)d*e ddd+ZdS),N)api)make_cooler_view)read_viewframe_from_file)cli cool_path COOL_PATH)metavartypenargsz--nprocz-pzPNumber of processes to split the work between.[default: 1, i.e. no process pool])helpdefaultr z --chunksizez-czFControl the number of pixels handled by each worker process at a time.gcAT)rr r show_defaultz--outputz-oz?Specify output file name to store the expected in a tsv format.F)rr requiredz--viewz --regionsaMPath to a 3 or 4-column BED file with genomic regions to calculated cis-expected on. When region names are not provided (no 4th column), UCSC-style region names are generated. Cis-expected is calculated for all chromosomes, when this is not specified. Note that '--regions' is the deprecated name of the option. Use '--view' instead.)existsz--smoothzeIf set, cis-expected is smoothed and result stored in an additional column e.g. balanced.avg.smoothed)ris_flagz--aggregate-smoothedzIf set, cis-expected is averaged over all regions and then smoothed. Result is stored in an additional column, e.g. balanced.avg.smoothed.agg. Ignored without smoothingz--smooth-sigmazjControl smoothing with the standard deviation of the smoothing Gaussian kernel, ignored without smoothing.g?z--clr-weight-namezqUse balancing weight with this name stored in cooler.Provide empty argument to calculate cis-expected on raw dataweightz--ignore-diagsz3Number of diagonals to neglect for cis contact typec Ttj|} |t| } nt|| d} tj| | d||||r|nd| || } |r| |ddddSt| ddddS) a Calculate expected Hi-C signal for cis regions of chromosomal interaction map: average of interactions separated by the same genomic distance, i.e. are on the same diagonal on the cis-heatmap. When balancing weights are not applied to the data, there is no masking of bad bins performed. COOL_PATH : The paths to a .cool file with a balanced Hi-C map. NT) check_sorting) view_df intra_onlysmoothaggregate_smoothed smooth_sigmaclr_weight_name ignore_diags chunksizenproc Fnan)sepindexna_rep) coolerCoolerrrrexpected expected_cisto_csvprint) r rroutputviewrrrrrclrrresults W/var/www/html/software/conda/lib/python3.11/site-packages/cooltools/cli/expected_cis.pyr(r( s@ - " "C |"3''+4DIII \ & & -!+:D!'  FB f$eE BBBBB fmmE%m@@AAAAA)r%r lib.commonrlib.iorclickrcommandargumentstroptionintPathfloatr(r0r/r=s ))))))------   [s!DDD   )  Q CII  J    Y 4     "    !   "    C   >  3B3B   EDP3B3B3Br0