DUf 8ddlZddlZddlZddlZddlmZddlmZm Z m Z m Z ddl m Z ddlmZddlmZd Zejejd d ejd ddejgdddejdddedejddddddejdd d!"ejd#d$d%d&ejd'd(d)eejd*d+ed,-ejd.d/d0dddejd1d2d3dddejd4d5dddejd6d7edejd8d9dd:ejd;dd?ed@dejdAdBdCDdEZdS)FN)api) CSRReaderDirectRangeQuery2DFillLowerRangeQuery2Dregion_to_extent) parse_region)cli)DelimitedTuplec&fd}|S)Ncbut} |}n=#t$r0}td|tjdYd}~nd}~wwxYwt j|ddg|d}r9t j| dg}|d|d z|d z|d < rt j| gd d}tj||gd } rdD]}||j vr||xxdz cc< rdD]}||j vr||xxdz cc<|S)NzColumn not found: r bin1_idbin2_idT)replaceweightweight1weight2countbalanced)chromstartend)axis)rr)start1start2) listKeyErrorprintsysexitrannotatepdconcatcolumns) chunk extra_fields extra_colseextradfcolr"rbinsjoin one_based_idsone_based_startss L/var/www/html/software/conda/lib/python3.11/site-packages/cooler/cli/dump.py annotatorz!make_annotator..annotators  >>L !,/    0Q00111  Ly),-z4E  OeT8*%566B "9 9 =g NE*   WL-F-F-F(GQUVVVE  Iuen1555E  $- $ $%-''#JJJ!OJJJ  $+ $ $%-''#JJJ!OJJJ s A&AA)r-rr.r"r/r0r2s`````` r1make_annotatorr4sC          D cool_uri COOL_PATH)metavarz--tablez-tzWhich table to dump. Choosing 'chroms' or 'bins' will cause all pixel-related options to be ignored. Note that for coolers stored in symmetric-upper mode, 'pixels' only holds the upper triangle values of the matrix.)chromsr-pixelsr:T)helptypedefault show_defaultz --columnsz-czKRestrict output to a subset of columns, provided as a comma-separated list.,)sep)r;r<z--headerz-Hz2Print the header of column names as the first row.F)r;is_flagr=r>z--na-repz1Missing data representation. Default is empty ''.)r;r=z--float-formatz@Format string for floating point numbers (e.g. '.12g', '03.2f').g)r;r=r>z--rangez-rzThe coordinates of a genomic region shown along the row dimension, in UCSC-style notation. (Example: chr1:10,000,000-11,000,000). If omitted, the entire contact matrix is printed.z--range2z-r2zThe coordinates of a genomic region shown along the column dimension. If omitted, the column range is the same as the row range.)r<r;z --fill-lowerz-fzFor coolers using 'symmetric-upper' storage, populate implicit areas of the genomic query box by generating lower triangle pixels. If not specified, only upper triangle pixels are reported. This option has no effect on coolers stored in 'square' mode.z--balanced/--no-balancez-bzRApply balancing weights to data. This will print an extra column called `balanced`z--joinzPrint the full chromosome bin coordinates instead of bin IDs. This will replace the `bin1_id` column with `chrom1`, `start1`, and `end1`, and the `bin2_id` column with `chrom2`, `start2` and `end2`.z --annotatezJoin additional columns from the bin table against the pixels. Provide a comma separated list of column names (no spaces). The merged columns will be suffixed by '1' and '2' accordingly.z--one-based-idsz2Print bin IDs as one-based rather than zero-based.)r;rAr=z--one-based-startszzdump..sW   L"Iu5         r5%T  F)r@lineterminatorindexheader float_formatna_rep)rCoolerr stdoutendswithgzipopenr9rr-lenr%rstderrr!rr _chromidsr chromsizesrJ storage_moderrr4mapto_csvflush)"r6tabler%rVrXrWrangerange2 fill_lowerrr.r"r/r0 chunksizeoutclrfselectorchunksr-n_binsh5readeri0i1j0j1bboxenginer2is_first_chunkr&rOs" @r1dumprz9sV *X  C {cSjj J e   Ic4  cNN ::<<  W .H111+ &88::  W .H111+xxzz!!!}T  D I   44 /cj A A A A HQKKK XXc]]2h<,A)B111)EFF  *% UCN33 FB !)M 88K BBRBB#DDvq&)D  H#*.???*65$ JJFF'tYGGF          ,t ,x ,&hh ?OIF++F\) N  # ac !!#'!-!"#N %       r5)r\r clickpandasr#rBrcorerrrrutilr r _utilr r4commandargumentoptionChoicestrintrzr3r5r1rs(   !!!!!!###L  K000    222 3 3      C  =   HRT K     8   A  1          K   F C  =     G     H   ; DD        10fDDDr5