DUf(ddlZddlZddlmZddlmZddlmZddlmZddl Z ej ej dd e d ej d d d e ejdddde ejddde dejdddejddejdde ddejd d!e d"dejd#d$ed%dejd&d'e ddejd(d)e ddejd*d+d,ejd-d.d,ejd/d0e d1dejd2d3d,ejd4d5dd6d7ZdS)8N)cli)api)make_cooler_view)read_viewframe_from_filein_pathIN_PATH)metavartypenargswindowWINDOW)r r r z--nprocz-pzPNumber of processes to split the work between.[default: 1, i.e. no process pool])helpdefaultr z--outputz-ozASpecify output file name to store the insulation in a tsv format.F)rr requiredz--viewz --regionsaPath to a BED file containing genomic regions for which insulation scores will be calculated. Region names can be provided in a 4th column and should match regions and their names in expected. Note that '--regions' is the deprecated name of the option. Use '--view' instead. T)existsz--ignore-diagszjThe number of diagonals to ignore. By default, equals the number of diagonals ignored during IC balancing.)rr r show_defaultz--clr-weight-namezxUse balancing weight with this name. Provide empty argument to calculate insulation on raw data (no masking bad pixels).weightz--min-frac-valid-pixelszgThe minimal fraction of valid pixels in a sliding diamond. Used to mask bins during boundary detection.gQ?z--min-dist-bad-binzwThe minimal allowed distance to a bad bin. Use to mask bins after insulation calculation and during boundary detection.z --thresholdzRule used to threshold the histogram of boundary strengths to exclude weakboundaries. 'Li' or 'Otsu' use corresponding methods from skimage.thresholding.Providing a float value will filter by a fixed thresholdz--window-pixelsz=If set then the window sizes are provided in units of pixels.)ris_flagz--append-raw-scoreszXAppend columns with raw scores (sum_counts, sum_balanced, n_pixels) to the output table.z --chunksizei-1z --verbosezReport real-time progress.z--bigwigzoAlso save insulation tracks as a bigWig files for different window sizes with the names output..bw)rrrctj|t}||}nt|d}| rfd|D}tj||||r|nd|||| | | | }|r||ddd n%t|ddd | r;|D]:}tj |j |d zt|zd zd | 9dSdS)a Calculate the diamond insulation scores and call insulating boundaries. IN_PATH : The path to a .cool file with a balanced Hi-C map. WINDOW : The window size for the insulation score calculations. Multiple space-separated values can be provided. By default, the window size must be provided in units of bp. When the flag --window-pixels is set, the window sizes must be provided in units of pixels instead. NT) check_sortingc0g|]}|jdzS)zbin-size)info).0winclrs U/var/www/html/software/conda/lib/python3.11/site-packages/cooltools/cli/insulation.py zinsulation..s%???#,,???) view_df window_bp ignore_diagsclr_weight_namemin_frac_valid_pixelsmin_dist_bad_bin thresholdappend_raw_scores chunksizeverbosenproc Fnan)sepindexna_rep.z.bwlog2_insulation_score_) value_field) coolerCoolerrrr insulationto_csvprintbioframe to_bigwig chromsizesstr)r routputviewr%r&r'r(r) window_pixelsr*r+r,bigwigr-cooler_view_dfr# ins_tablewrs @r r8r8 syn - C&c**N | +4DIII@???????)) !+:D3)+*  I ETuEEEE i4uUCCDDD  A   s1vv%-8Q88        r")clickr6rrr lib.commonrlib.iorr;commandargumentr>intoptionPathfloatr8r"r rPsR ))))))------  93a@@@H3???   )  L    Z 4     <   Z   3    S   ?  H      m"3tTTT k