o Nrf" @sddlZddlmZddlZddlZddlmZddlmZddl m Z e ej ddd ej d d d ej d d d ej ddddej dddddddej ddeddgdde dddZdS) N)util)cli)exit_on_broken_pipe chromsizesZCHROMSIZES_PATH)metavarfastaZ FASTA_PATHenzymeZENZYMEz--outz-oz Output file (defaults to stdout))helpz--headerz-Hz2Print the header of column names as the first row.TF)r Zis_flagdefaultZ show_defaultz --rel-idsz-i01ziInclude a column of relative bin IDs for each chromosome. Choose whether to report them as 0- or 1-based.)typer c Cstj|dd}t|}t|r(tt|d}|tt|dn|g}tj |g|R}t ||} |durU| d | d<t |dkrU| dd7<|dur]tj} nt|d } |rr| d d j| d d d dd| j| 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)Z all_namesz*.faz*.fastaNZchromidrwr  F)seplineterminatorindexheader)rZread_chromsizeslistkeysopisdirglobjoinextendZ load_fastadigestgroupbyZcumcountintsysstdoutopenZto_csvflush) rr r outrZrel_idsZchromsZ filepathsZ fasta_recordsZfragsfr(Z/var/www/html/software/conda/envs/catlas/lib/python3.10/site-packages/cooler/cli/digest.pyr s*$        r)rZos.pathpathrr"ZclickrrZ_utilrcommandargumentoptionZChoicerr(r(r(r)s8