tf"ddlZddlmZddlZddlZddlmZddlmZddl m Z ejejdd ejd d ejd d ejdddejddddddejddejddgde ddZy)N)util)cli)exit_on_broken_pipe chromsizesCHROMSIZES_PATH)metavarfasta FASTA_PATHenzymeENZYMEz--outz-oz Output file (defaults to stdout))helpz--headerz-Hz2Print the header of column names as the first row.TF)ris_flagdefault show_defaultz --rel-idsz-i01ziInclude a column of relative bin IDs for each chromosome. Choose whether to report them as 0- or 1-based.)typerctj|d}t|j}t j |rbt j t j|d}|jt j t j|dn|g}tj|g|}tj||} |=| jdj| d<t|dk(r | dxxdz cc<|tj} n t!|d } |r| d d j#| d d d d| j#| d d d d | j%y)ab Generate fragment-delimited genomic bins. Output a genome segmentation of restriction fragments as a BED file. CHROMSIZES_PATH : UCSC-like chromsizes file, with chromosomes in desired order. FASTA_PATH : Genome assembly FASTA file or folder containing FASTA files (uncompressed). ENZYME : Name of restriction enzyme T) all_namesz*.faz*.fastaNchromidrwr  F)seplineterminatorindexheader)rread_chromsizeslistkeysopisdirglobjoinextend load_fastadigestgroupbycumcountintsysstdoutopento_csvflush) rr r outr rel_idschroms filepaths fasta_recordsfragsfs [/var/www/html/software/conda/envs/higlass/lib/python3.12/site-packages/cooler/cli/digest.pyr*r* s:H%%jDAJ *//# $F xxIIbggeV45 2775)#<=>G OOF7Y7M KK v .EmmG,557d w<1  $K1 K { JJ cN  a  4E$   LLTuLMGGI)r&os.pathpathr$r.clickrr_utilrcommandargumentoptionChoicer*r;r:rFs  &  &78.(+ gt"DE  =    sCj ! 6 Q-F,/9*-r;