tft/ddlmZddlZddlZddlZddlZddlmZddl Z ddl Z ddl Z ejeZ ddZ ddZy))print_functionNcg}|D]H} tj| ddk(r|tj| dgz }9|t| dgz }Jtj } |} g} d} d}|r|dj d}td|tt|D]\}}|djds|djd r0|||\}}}}t|t||zkrEtjd ||tj gt||zt|z zz }||zdk7r+tjd |tj d|2||k7r-t j"| ||||t| zd} d}g} |}||z}| |kr| | gt|zgz } | dz } | |kr | |k7rd j%|||}t'|t)j*||z }| |kr| |gz } | dz } | |krt| | k\s t j"| ||||t| zg} | }td||t j"| |||t| zy#t,$rB}td |tj.tdtj.Yd}~yd}~wwxYw)z9 Convert an epilogos bedfile to multivec format. z.gzrtrrNzbase_resolution:browsertrackz-Lines contain fewer columns than expected: %szDThe start coordinate is not a multiple of the resolution in line: %sz The expected position location does not match the observed location at entry {}:{}-{} This is probably because the bedfile is not sorted. Please sort and try again. zError:filez-Probably need to set the --num-rows parameterzdumping batch:)opsplitextgzipopennpnanreadlineprint enumeratezip startswithlenloggerwarningerrorsysexitarrayformat ValueErrormathceil TypeErrorstderr)input_filenamesf_out!bedline_to_chrom_start_end_vectorbase_resolution has_header chunk_sizenum_rows row_infosfilesinput_filename FILL_VALUE batch_lengthbatch curr_indexbatch_start_index prev_chrom_lineschromstartendvectordata_start_indexmessagedata_end_indexexs Z/var/www/html/software/conda/envs/higlass/lib/python3.12/site-packages/clodius/multivec.pybedfile_to_multivecr?s2 E)1 ;;~ &q )U 2 dii56 6E d>3/0 0E 1 JL EJ aJ o.c5k*X>5 8  y )U1X-@-@-I $EeY$W!uc6 v;Uh. . NNJE R rvvh#e*x"7#f+"EF FF ? "a ' LLV  HHQK  !ez&9 * !$5E $B  J ! E !O3++ zlS[01 1E !OJ++ ) )uc  W% %3#89>) fX E !OJ>) u: % HHUOe %(9CJ(FE *  "E+< =qX>tHJxxPUE%L"%6U%CD h4ECJJW s-'J K7KKc : |}tj|rtj|t j |d}|j d||djd<|j d|j d|} |dj t| t|\} } tj| d} d|jvr|jd}|+|dt| jjd||dt| j d|dt| j d |dt| djd t| f| j| d |dt| djd t| f| d |djd t| f| j| d |djd t| f| d t| | D]\} }| |vr+t!dj#| t$j&6|dt| d jt| || j(d d}d}|dt| d | }t+t-|t|}|t|ks|| |||z||||z|t+t-|t|| |z z }|t|krGt/| }t1j2t1j4|||zz t1j4dz }| }t7|D]}|dz} |dj t| |+|dt| jjd||dt| j d|dt| j d |dt| djd t| f| j| d |dt| djd t| f| d t| | D]\} }| |dt|d vrd}|dt|d | }d}t+t-|t|}t9|j(}t1j2|ddz |d<t;|}|dt| d j| |d |t|ks|dt|d | |||z}t|dzdk7r tj<||dgf}|dz }||} ||dt| d | t+|dz t+|dz |dz z|t+t-|t||z z }|t|kr| }|S)a Create a multires file containing the array data aggregated at multiple resolutions. Parameters ---------- array_data: {'chrom_key': np.array, } The array data to aggregate organized by chromosome chromsizes: [('chrom_key', size),...] agg: lambda The function that will aggregate the data. Should take an array as input and create another array of roughly half the length starting_resolution: int (default 1) The starting resolution of the input data tile_size: int The tile size that we want higlass to use. This should depend on the size of the data but when in doubt, just use 256. winfoz tile-size resolutionschromsS)dtyper+valuesnamer)shaperFdata compressionlength)rIrJrKzMissing chrom {} in input filer )rKgj@rr)r existsosremoveh5pyFile create_groupattrsstrrrrcreatecreate_datasetrrFrrrr#rIintminsumr r!lograngelisttuple concatenate) array_data chromsizesaggstarting_resolution tile_size output_filer+filenamefcurr_resolutionrDlengths chrom_arrayr6rLstandard_chunk_sizer7 chrom_datar) total_lengthmax_zoomprev_resolutioni new_shapeold_datanew_datas r>create_multivec_multiresrus:H yy ( (C ANN6#,AfIOOK NN=!NN8*O m!!#o"67:&OFG((6-Kj&&&$$[1  -_-.44;;KSmS)*77AmS)*77AmS)*84CC6{n  DmS)*84CCVW&DhK6{n  hKVW& VW-S v  " 299%@szz R  -_-.x8GG J 5)//V H "}%c/&:;HEeL 0#j/BC c*o%5?5F *6Juuz1 2 S0#j6G2H52PQR RE c*o%!S4w?I%PJ"% S!4c*oFGJZ--.I99Yq\A%56IaLi(I m S1 28 < K Kyf L #j/)]+C,@A(KEREJ.x=1$) "~~x(2,.HIH!OJx=- _!56x@G NSZ!^)C%DS!4c*o6MNOOC#j/)-7 Pr*aP*b H)N)riz/tmp/my_file.multiresN) __future__rrloggingr rPos.pathpathr rrRnumpyr getLogger__name__rr?rurvr>rsS%      8 $@WN'O rv