DUf"ddlZddlmZddlZddlZddlmZddlmZddl m Z ej ej dd ej d d ej d d ej dddej ddddddej ddejddgde ddZdS)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.)typerc4tj|d}t|}t j|rbt jt j|d}|t jt j|dn|g}tj |g|R}tj ||} |M| d | d<t|dkr| dxxdz cc<| tj} nt!|d } |r"| d d | d d d d| | d d d d | dS)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 N/var/www/html/software/conda/lib/python3.11/site-packages/cooler/cli/digest.pyr*r* sH%jDAAAJ *//## $ $F xIbgeV4455 275)#<#<==>>>>G OF7Y777M K v . .EmmG,,5577d w<<1   $KKK1 KKK { J cNN   ac  4E$     LLTuLMMMGGIIIII)r&os.pathpathr$r.clickrr_utilrcommandargumentoptionChoicer*r;r:rFs  &&&&&&  &7888...(+++ gt"DEEE  =    sCj ! ! 6 Q--FE,+/.98*---r;