DUfddlZddlZddlZddlZddlmZddlm Z ddl m Z ddl Z ddl mZmZddlmZeje jd d e e jd d eddde jddddee jddedde jddedde jddedde jdd d!dd"#e jd$d%d&d'e jd(d)dd"#d*ZdS)+N) eigdecomp)make_cooler_view)read_viewframe_from_file)TabularFilePathsniff_for_header)cli cool_path COOL_PATH)metavartypez--phasing-trackziPhasing track for orienting and ranking eigenvectors,provided as /path/to/track::track_value_column_name.T)existsdefault_column_index TRACK_PATH)helprr z--viewz --regionszPath to a BED file which defines which regions of the chromosomes to use (only implemented for cis contacts). Note that '--regions' is the deprecated name of the option. Use '--view' instead. )rdefaultrz--n-eigsz"Number of eigenvectors to compute.)rrr show_defaultz--clr-weight-namezkUse balancing weight with this name. Using raw unbalanced data is not currently supported for eigenvectors.weightz--ignore-diagszjThe number of diagonals to ignore. By default, equals the number of diagonals ignored during IC balancing.z-vz --verbosezEnable verbose outputF)ris_flagrz-oz --out-prefixzSave compartment track as a BED-like file. Eigenvectors and corresponding eigenvalues are stored in out_prefix.contact_type.vecs.tsv and out_prefix.contact_type.lam.txt)rrequiredz--bigwigzZAlso save compartment track (E1) as a bigWig file with the name out_prefix.contact_type.bwc jtj|} |s|\} } t| \} } | Yt| ts't jd| d}tdddd| gddd |g }nt| trS | | } n#t$r<t jd | d | wxYw| | vr;t jd | d | | }tdddd |g}tj | fdtdtjd tj|tjid|d|}|}|t#| }|}nt%|| d}t'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#)dtypecommentverboseT) check_sortinggX@)clr phasing_trackview_dfn_eigsclr_weight_name ignore_diagsclip_percentile sort_metricz.cisz.lam.txt F)sepindexz .vecs.tsvz.bwE1) value_field)coolerCoolerr isinstanceintclick BadParameterformatdict IndexErrorjoinpd read_tablestrnpint64float64rrreigs_cisto_csvbioframe to_bigwig chromsizes)r r)viewr+r,r-r& out_prefixbigwigr( track_pathcolbufr track_namekwargstrack_dfcooler_view_dfr*eigvals eigvec_tables S/var/www/html/software/conda/lib/python3.11/site-packages/cooltools/cli/eigs_cis.pyrErEsl - " "C ( C%j11 U =c3'' (@@Fs  JAq# ;FF #s## *CC!,ELL%e##,>EE% J7GUJ2WXXXF=   rxBJ        !  |)#.. *4DIII&. #'!   G\ NN:&3UNKKK V+k9t5QQQ    N  % '         s B))AC/)pandasr?numpyrBr5rGapir lib.commonrlib.iorr9utilrr r commandargumentrAoptionr8rErVrcs ))))))------ 33333333  [s;;;  ; 1 = = =    Z   -   M   <  +3T5 L  0   q q <;vq q q rb