DUfLddlZddlZddlZddlmZddlmZddlmZej ej dde d ej d d e d ej d d dde ej ddde ej ddde ej ddde ej dde e ddej dddejddgd d!ZdS)"N)api)cli)sniff_for_headerin_pathIN_PATH)metavartypenargsout_pathOUT_PATHz--viewzPath to a BED-like file which defines which regions of the chromosomes to use and in what order. Using --new-chrom-col and --orientation-col you can specify the new chromosome names and whether to invert each region (optional)T)helpdefaultrequiredr z--new-chrom-colzColumn name in the view with new chromosome names. If not provided and there is no column named 'new_chrom' in the view file, uses original chromosome names)rrr z--orientation-colzColumns name in the view with orientations of each region (+ or -). If not providedand there is no column named 'strand' in the view file, assumes all are forward orientedz --assemblyz^The name of the assembly for the new cooler. If None, uses the same as in the original cooler.z --chunksizezBThe number of pixels loaded and processed per step of computation.gcA)rr r show_defaultz--modez3(w)rite or (a)ppend to the output file (default: w)waF)case_sensitivec  tj|}gd} t|\} } | tj| dd} ntj| | d} | j} |d}n|| jvrtd|d |d }n|| jvrtd |d | || d | |<| |d | |<tj || ||||||dS)a5Rearrange data from a cooler according to a new genomic view Parameters ---------- IN_PATH : str .cool file (or URI) with data to rearrange. OUT_PATH : str .cool file (or URI) to save the rearrange data. view : str Path to a BED-like file which defines which regions of the chromosomes to use and in what order. Has to be a valid viewframe (columns corresponding to region coordinates followed by the region name), with potential additional columns. Using --new-chrom-col and --orientation-col you can specify the new chromosome names and whether to invert each region (optional). If has no header with column names, assumes the `new-chrom-col` is the fifth column and `--orientation-col` is the sixth, if they exist. new_chrom_col : str Column name in the view with new chromosome names. If not provided and there is no column named 'new_chrom' in the view file, uses original chromosome names. orientation_col : str Columns name in the view with orientations of each region (+ or -). - means the region will be inverted. If not providedand there is no column named 'strand' in the view file, assumes all are forward oriented. assembly : str The name of the assembly for the new cooler. If None, uses the same as in the original cooler. chunksize : int The number of pixels loaded and processed per step of computation. mode : str (w)rite or (a)ppend to the output file (default: w) )chromstartendname new_chromstrandNr )headersep)namesrrzNew chrom col z not found in view columnsrzOrientation col r+) new_chrom_colorientation_colassembly chunksizemode) coolerCoolerrpd read_tableread_csvcolumns ValueErrorfillnar rearrangerearrange_cooler) rr viewr"r#r$r%r&clr default_namesbufr view_dfs T/var/www/html/software/conda/lib/python3.11/site-packages/cooltools/cli/rearrange.pyr/r/ sYh - CLLLM!$''JC -A4888+cDAAA# go - -S-SSSTTT"  / /WOWWWXXX %]3::77;KLLGM&7>>sCCGOM"" #' #     )clickr'pandasr)rrutilrcommandargumentstroptionintChoicer/r7r6rCs """"""  93a@@@ JSBBB   I    !         M CHH  >  sCj 7 7 7  HH CBA@`HHHr7