DUf+ddlZddlZddlZddlZddlZddlm Z m Z m Z m Z m Z ddlmZmZddlmZmZmZejejdd ejd ejd d d ejdd ejdddejddgd ejddejddejdded ejdd d d!"ejd#d d d$"ejd%ed&d d'(ejd)d*d+d d ,ejd-ejd.d/gd.d0d 1ejd2d3d4ed56ejd7d8e9ejd:d;ejd d d d <9ejd=d>ed?d @ejdAdBd d ,ejdCdDejdEdFd d dG"dHZdS)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| dkrd}n| dkrd}|;t|5}t j|}dddn #1swxYwYddg}t t td}|d krgd }tttttt|d d }| d d| dd| dd| dd| dd| dddd (t|d ||d}n9|dkr3ddg}tt|d d}dddd(t|||d}t|r|D]}t|d\} }!}"}#|!_| d vr|"|"|| <&| d kr7|"5|d |d |"|| <|"|| <ct!jd!|"| |vr|| | |vr|| |!(| <|" |"|| <|"|| <n*|d |d d |vr |rt$j|d <t$j|d <|Ht)|}$|$D]5}%t+|$|%t,rt/|$|%|$|%<6nd}$|d#kr t0j}&n|}&t5j|&d$(fd%|D||| d| &}'|d'(|d(||d)|t;||t=||'||||| ||| d|rdnd||$|rd*nd+,dS)-a Create a cooler from a pre-binned matrix. BINS_PATH : One of the following : 1. Path to a chromsizes file, 2. Bin size in bp : Path to BED file defining the genomic bin segmentation. PIXELS_PATH : Text file containing nonzero pixel values. May be gzipped. Pass '-' to use stdin. COOL_PATH : Output COOL file path or URI. **Notes** Two input format options (tab-delimited). Input pixel file may be compressed. COO: COO-rdinate sparse matrix format (a.k.a. ijv triple). 3 columns: "bin1_id, bin2_id, count", BG2: 2D version of the bedGraph format. 7 columns: "chrom1, start1, end1, chrom2, start2, end2, count" **Examples** cooler load -f bg2 : in.bg2.gz out.cool Nr"reflectr#dropbin1_idbin2_id)r*r+countr)chrom1start1end1chrom2start2end2r,)r-r.r/r0r1r2r,r-rr.r r/rr0r1r2T)schema is_one_based tril_actionsortr)r8r9r:F) includes_agg>r*r+zA field number is required.) param_hint- c g|] }| Sr@).0nameinput_field_numberss L/var/www/html/software/conda/lib/python3.11/site-packages/cooler/cli/load.py zload..MsIIIt$T*III)sepusecolsnamesdtypecommentiterator chunksizezfields: zdtypes: zsymmetric-upper: aw) columnsdtypesmetadataassemblymergebuf max_mergetemp_dir delete_temp ensure_sorted triuchecksymmetric_upperh5optsmode)r __name__r openjsonloadrrstrintgetrrlenr appendclick BadParameternpfloat64r isinstancelisttuplesysstdinpdread_csvinformap))rrrformatrRrSfieldcount_as_float one_based comment_charinput_copy_statusno_symmetric_upperrMrTrUrVno_delete_tempstorage_optionsrekwargslogger chromsizesbinsrZr9foutput_field_namesoutput_field_dtypesinput_field_namesinput_field_dtypespipelineargrBcolnumrJ_r[keyf_inreaderrCs) @rDr`r`s[\ ! !F!),,J,,OK!  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