DUfNddlZddlZddlZddlZddlmZddlm Z ddl Z ddl m Z m Z ddlmZeje jdd e e jd d e d dde jddddee jddedd e jddedd e jdddd d e jd!d"d#d $e jd%d&d d d'ZdS)(N) eigdecomp)make_cooler_view)TabularFilePathsniff_for_header)cli cool_path COOL_PATH)metavartypez--phasing-trackziPhasing track for orienting and ranking eigenvectors,provided as /path/to/track::track_value_column_name.T)existsdefault_column_index TRACK_PATH)helpr r z--viewz --regionszPath to a BED file which defines which regions of the chromosomes to use (only implemented for cis contacts). Note that '--regions' is the deprecated name of the option. Use '--view' instead. )rdefaultr z--n-eigsz"Number of eigenvectors to compute.)rr r show_defaultz--clr-weight-namez\Use balancing weight with this name. Using raw unbalanced data is not supported for saddles.weightz-vz --verbosezEnable verbose outputF)ris_flagrz-oz --out-prefixzSave compartment track as a BED-like file. Eigenvectors and corresponding eigenvalues are stored in out_prefix.contact_type.vecs.tsv and out_prefix.contact_type.lam.txt)rrequiredz--bigwigzZAlso save compartment track (E1) as a bigWig file with the name out_prefix.contact_type.bwc `tj|}t|} |s|\} } t| \} } | Yt | t s't jd| d}tdddd| gddd |g }nt | t rS | | } n#t$r<t jd | d | wxYw| | vr;t jd | d | | }tdddd |g}tj | fdtdtjd tj|tjid|d|}|}|| }nt%dt'j||||dd\}}||dzdzdd||dzdzdd|r%t-j||j|dzdzddSdS)a Perform eigen value decomposition on a cooler matrix to calculate compartment signal by finding the eigenvector that correlates best with the phasing track. COOL_PATH : the paths to a .cool file with a balanced Hi-C map. Use the '::' syntax to specify a group path in a multicooler file. TRACK_PATH : the path to a BedGraph-like file that stores phasing track as track-name named column. BedGraph-like format assumes tab-separated columns chrom, start, stop and track-name. Nz:No header found. Cannot find "{}" column without a header.refrrrchromstartend)headerusecolsnamesz+Column #{} not compatible with header "{}".,z$Column "{}" not found in header "{}"infer)rr#)dtypecommentverbosez6views are not currently implemented for CLI eigs-trans)clr phasing_trackn_eigsclr_weight_name partition sort_metricz.transz.lam.txt F)sepindexz .vecs.tsvz.bwE1) value_field)coolerCoolerrr isinstanceintclick BadParameterformatdict IndexErrorjoinpd read_tablestrnpint64float64NotImplementedErrorr eigs_transto_csvbioframe to_bigwig chromsizes)r r'viewr(r)r% out_prefixbigwigr&cooler_view_df track_pathcolbufr track_namekwargstrack_dfview_dfeigvals eigvec_tables U/var/www/html/software/conda/lib/python3.11/site-packages/cooltools/cli/eigs_trans.pyrBrB sX - " "C%c**N ( C%j11 U =c3'' (@@Fs  JAq# ;FF #s## *CC!,ELL%e##,>EE% J7GUJ2WXXXF=   rxBJ        !  | ! D   &0 #' G\ NN:(:54uNMMM X- ;USSS    N  !E )         s /B88AC>)pandasr;numpyr>r1rDapir lib.commonrr5utilrrr commandargumentr=optionr4rBrTr`s= )))))) 33333333  [s;;;  ; 1 = = =    Z   -   g  +3T5 L  0   r r <;dr r r r_