o NrfS @sddlZddlZddlmZddlmZddlmZeejde dd ejd e d d ej d d ddej dddddddej dde ddgddedddZ dS)N)util)cli)exit_on_broken_pipe chromsizesZCHROMSIZES_PATH)typemetavarbinsizeZBINSIZEz--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.)rr cCstj|dd}t||}|dur*|jddd|d<t|dkr*|dd7<|dur2tj}nt|d}|rG|d d j |d d d dd |j |d d d d d | dS)a Generate fixed-width genomic bins. Output a genome segmentation at a fixed resolution as a BED file. CHROMSIZES_PATH : UCSC-like chromsizes file, with chromosomes in desired order. BINSIZE : Resolution (bin size) in base pairs . T)Z all_namesNZchrom)Zobservedidrwr  F)seplineterminatorindexheader) rZread_chromsizesZbinnifygroupbyZcumcountintsysstdoutopenZto_csvflush)rr outrZrel_idsZbinsfr\/var/www/html/software/conda/envs/catlas/lib/python3.10/site-packages/cooler/cli/makebins.pymakebins s      r!)rZclickrrZ_utilrcommandargumentstrroptionZChoicer!rrrr s2