DUf ddlZddlmZddlmZddlmZddlZddlmZej ej dd e d ej d d d de ej ddde e ddej ddde dej dddejddej dde d dd!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 --regionsaPath to a 3 or 4-column BED file with genomic regions. Trans-expected is calculated on all pairwise combinations of these regions. When region names are not provided (no 4th column), UCSC-style region names are generated. Trans-expected is calculated for all inter-chromosomal pairs, when view is not specified. Note that '--regions' is the deprecated name of the option. Use '--view' instead.)existsz--clr-weight-namezqUse balancing weight with this name stored in cooler.Provide empty argument to calculate cis-expected on raw dataweightcJtj|}|t|}nt||d}tj|||r|nd||}|r||ddddSt|ddddS) a| Calculate expected Hi-C signal for trans regions of chromosomal interaction map: average of interactions in a rectangular block defined by a pair of regions, e.g. inter-chromosomal blocks. 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_dfclr_weight_name chunksizenproc Fnan)sepindexna_rep) coolerCoolerrrrexpectedexpected_transto_csvprint) r rroutputviewrclrrresults Y/var/www/html/software/conda/lib/python3.11/site-packages/cooltools/cli/expected_trans.pyr"r" sB - " "C |"3''+4DIII \ ( ( +:D )FB f$eE BBBBB fmmE%m@@AAAAA)rr lib.commonrlib.iorclickrcommandargumentstroptionintPathr"r*r)r6s ))))))------   [s!DDD   )  Q CII  J    Y 4     C  *B*B  EDZ*B*B*Br*