tf+ddlZddlZddlZddlZddlZddlm Z m Z m Z m Z m Z ddlmZmZddlmZmZmZej*ej,dd ej,d ej.d d d ej,dd ej0dddej2ddgd ej0ddej0ddej0dded ej0dd d d!"ej0d#d d d$"ej0d%ed&d d'(ej0d)d*d+d d ,ej0d-ej2d.d/gd.d0d 1ej0d2d3d4ed56ej0d7d8e9ej0d:d;ej.d d d d <9ej0d=d>ed?d @ej0dAdBd d ,ej0dCdDej0dEdFd d dG"dHZy)IN) BIN_DTYPE COUNT_DTYPEcreate_from_unorderedsanitize_pixelssanitize_records)cli get_logger) parse_binsparse_field_paramparse_kv_list_param bins_path BINS_PATH)metavar pixels_pathT)exists allow_dash PIXELS_PATH)typer cool_path COOL_PATHz--formatz-fz'coo' refers to a tab-delimited sparse triplet file (bin1, bin2, count). 'bg2' refers to a 2D bedGraph-like file (chrom1, start1, end1, chrom2, start2, end2, count).coobg2)helprrequiredz --metadataz+Path to JSON file containing user metadata.)rz --assemblyz)Name of genome assembly (e.g. hg19, mm10)z--fieldaAdd supplemental value fields or override default field numbers for the specified format. Specify quantitative input fields to aggregate into value columns using the syntax ``--field =``. Optionally, append ``:`` followed by ``dtype=`` to specify the data type (e.g. float). Field numbers are 1-based. Repeat the ``--field`` option for each additional field.)rrmultiplez--count-as-floatFz{Store the 'count' column as floating point values instead of as integers. Can also be specified using the `--field` option.)is_flagdefaultrz --one-basedzWPass this flag if the bin IDs listed in a COO file are one-based instead of zero-based.z--comment-char#z1Comment character that indicates lines to ignore.)rr show_defaultrz--no-symmetric-upperz-NztCreate a complete square matrix without implicit symmetry. This allows for distinct upper- and lower-triangle values)rrrz--input-copy-statusuniqueduplexaCopy status of input data when using symmetric-upper storage. | `unique`: Incoming data comes from a unique half of a symmetric matrix, regardless of how element coordinates are ordered. Execution will be aborted if duplicates are detected. `duplex`: Incoming data contains upper- and lower-triangle duplicates. All lower-triangle input elements will be discarded! | If you wish to treat lower- and upper-triangle input data as distinct, use the ``--no-symmetric-upper`` option instead. )rrrr!z --chunksizez-czSize in number of lines/records of data chunks to read and process from the input stream at a time. These chunks will be saved as temporary partial coolers and then merged.i-1)rrrz --mergebufzgTotal number of records to buffer per epoch of merging data. Defaults to the same value as `chunksize`.)rrz --temp-dirzaCreate temporary files in a specified directory. Pass ``-`` to use the platform default temp dir.)r file_okaydir_okayrz --max-mergez3Maximum number of chunks to merge in a single pass.)rrrr!z--no-delete-tempz,Do not delete temporary files when finished.z--storage-optionszOptions to modify the data filter pipeline. Provide as a comma-separated list of key-value pairs of the form 'k1=v1,k2=v2,...'. See http://docs.h5py.org/en/stable/high/dataset.html#filter-pipeline for more details.z--appendz-az_Pass this flag to append the output cooler to an existing file instead of overwriting the file.c tt}t|\}}| | } | }d}|r| dk(rd}n| dk(rd}|)t|5}t j |}dddddg}t t td}|d k(rgd }tttttt|d d }|jd d|jdd|jdd|jdd|jdd|jdddd }t|d ||d}n/|dk(r*ddg}tt|d d}dddd}t|||d}t|r|D]} t| d\}!}"}#}$|"W|!d vr|#|#||!<#|!d k(r/|#-jd |jd |#|!<|#||!<Wt!j"d!| "|!vr|j|!|!|vr|j|!|"|!<|#|#|!<|#||!<n"jd |jd d vr(|r&t$j&d <t$j&|d <|8t)|}%|%D]'}&t+|%|&t,st/|%|&|%|&<)nd}%|d#k(rt0j2}'n|}'t5j6|'d$|D!cgc]}!|! c}!|| d| %}(|j9d&|j9d'||j9d(|t;||t=|(||||| ||| d|rdnd||%|rd)+yd*+y#1swYxYwcc}!w),a Create a cooler from a pre-binned matrix. BINS_PATH : One of the following : 1. Path to a chromsizes file, 2. Bin size in bp : Path to BED file defining the genomic bin segmentation. PIXELS_PATH : Text file containing nonzero pixel values. May be gzipped. Pass '-' to use stdin. COOL_PATH : Output COOL file path or URI. **Notes** Two input format options (tab-delimited). Input pixel file may be compressed. COO: COO-rdinate sparse matrix format (a.k.a. ijv triple). 3 columns: "bin1_id, bin2_id, count", BG2: 2D version of the bedGraph format. 7 columns: "chrom1, start1, end1, chrom2, start2, end2, count" **Examples** cooler load -f bg2 : in.bg2.gz out.cool Nr"reflectr#dropbin1_idbin2_id)r*r+countr)chrom1start1end1chrom2start2end2r,)r-r.r/r0r1r2r,r-rr.r r/rr0r1r2T)schema is_one_based tril_actionsortr)r8r9r:F) includes_agg>r*r+zA field number is required.) param_hint- )sepusecolsnamesdtypecommentiterator chunksizezfields: zdtypes: zsymmetric-upper: aw) columnsdtypesmetadataassemblymergebuf max_mergetemp_dir delete_temp ensure_sorted triuchecksymmetric_upperh5optsmode)r __name__r openjsonloadrrstrintgetrrlenr appendclick BadParameternpfloat64r isinstancelisttuplesysstdinpdread_csvinformap))rrrformatrJrKfieldcount_as_float one_based comment_charinput_copy_statusno_symmetric_upperrErLrMrNno_delete_tempstorage_optionsr]kwargslogger chromsizesbinsrRr9foutput_field_namesoutput_field_dtypesinput_field_namesinput_field_dtypesinput_field_numberspipelineargnamecolnumrB_rSkeyf_inreaders) Y/var/www/html/software/conda/envs/higlass/lib/python3.12/site-packages/cooler/cli/load.pyrXrXs!\ !F!),J,,OK  (#K ( * K (^ $qyy|H $$Y/ (1 jj1-jj1-JJvq)jj1-jj1-JJvq) $ "#   5    (1  +,AF" yk   5z 2C%6s%O "D&%~11e6G05'-W_):%,,W5&--g6/4&t,05'-,,5#,,!((.--"))$/(.  % +0"4(,1#D)= 2D   )!!'*##&(jj7#')zzG$"$_5 1C&+t,#F3K0s  1cyy [[ 7HIt$T*I  F KK(./01 KK(-./0 KK#O#456  Hf""&&*$u'S%$!$%S $ $zJsM  M M)rer^numpyr`pandasrg simplejsonrWcreaterrrrrr r _utilr r rcommandargumentPathoptionChoicerYrZrXrrs EE  [1  $4@- [1  ; uen %  l!NO l!LM   ?     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