tf8ddlmZddlZddlZddlmZddlmZddlmZddl m Z m Z ddl Z ddl mZddlZddlZddlmZmZdd lmZd d lmZmZd d lmZmZgd Zd)dZ d*dZ! d+dZ"GddZ#Gdde#Z$ d, d-dZ%d.dZ&d/dZ'd0d1dZ(d2dZ)d3dZ*d3dZ+d4dZ, d5dZ-d6d7dZ.d6d7dZ/ d8 d9d Z0d:d!Z1Gd"d#eZ2Gd$d%Z3d;d&Z4dA H  H  JJsO"   H s6A** B4B  B BBBBBc.eZdZdddZddZd dZddZy) TreeNodeNc.||_||_||_yN)r1depthlevel)selfr1r7r8s r"__init__zTreeNode.__init__Cs  r$c@t|jjSr6)typer1__name__r9s r"get_typezTreeNode.get_typeHsDHH~&&&r$c0t|jdrz|j|j|jkrU|jdz}|jj }|Dcgc] }|j |||j"c}SgScc}w)Nvaluesr )r7r8)r,r1r8r7rA __class__)r9r7childrenr!s r" get_childrenzTreeNode.get_childrenKs} 488X &zz!TZZ$**%< Q88??,NVIJDNN1END s)%Bc|jjjddxsd}t|jdr3|d|jjd|jj z }|S)N/shape )r1namesplitr,rHdtype)r9rJs r"get_textzTreeNode.get_textUs`xx}}""3'+2s 488W % a'q(89 9D r$)rN)r1rr7intr8 int | Nonereturnr.)rQlist[TreeNode])r= __module__ __qualname__r:r?rDrMr$r"r4r4Bs 'r$r4ceZdZddZy)AttrNodecZ|jjjddxsdS)NrFrG)r1rJrKr>s r"rMzAttrNode.get_text]s%xx}}""3'+2s2r$NrP)r=rSrTrMrUr$r"rWrW\s3r$rWc>dfd t||}||iS)zALike :py:method:`h5py.Group.visititems`, but much faster somehow.c|j}|rO|D]J}||jj|j||jj<|||L|Sr6)rDr1rJ)nodefuncresultrCchild _visititemss r"r_zvisititems.._visititemshs[$$& ! 1)-eiinneii)Huyy~~&E40 1 r$r8r6)r4)groupr\r8rootr_s @r" visititemsrcas% E 'D tT2 &&r$cjjdd}|tk(r:d}tfd|Ds#t j dj dyy)Nformat)chromsbinspixelsindexesc3BK|]}|jvywr6keys).0rJgrps r" z_is_cooler..xs7$4388:%7z Cooler path z appears to be corruptTF)attrsgetrallwarningswarnrJ)rnfmtrls` r" _is_coolerrwtsQ ))--$ 'C e|67$77 MML 2HI J r$ct|\}}tj|sytj|5}t ||cdddS#1swYyxYw)z Determine if a URI string references a cooler data collection. Returns False if the file or group path doesn't exist. FN)rh5pyis_hdf5Filerw)urifilepath grouppathfs r"rr~sQ +3/Hi << ! 8 (!I,'(((s AActj|sytj|5}|jj dd}d|j vrdt |dj dkDrEtt|dj }|dk(rJt|d|r9 dddyd|j vrt|dr|d kr dddydddy#1swYyxYw) zg Determine if a file is a multi-res cooler file. Returns False if the file doesn't exist. FreN resolutionsrz HDF5::MCOOLT0) ryrzr{rqrrrllennextiterrw)r} min_versionrrvrJs r"rrs << ! 8 ggkk(D) AFFH $Q}-=-B-B-D)E)IQ}-22456Dm# 1]3CD3I(J  AFFH_AcF!3 a  sB C7?&C77Dc2tj|std|dtj|5jj dd}|t k(rd}tfd|Dstjd dddyd jvr\td jd kDr=d jD]}td |rdddy dddy dddy#1swYyxYw) zi Determine if a file is a single-cell cooler file. Returns False if the file doesn't exist. '' is not an HDF5 file.FreN)rfrgcellsc3BK|]}|jvywr6rk)rmrJrs r"roz is_scool_file..s9Dtqvvx'9rpz Scool file appears to be corruptrrT) ryrzOSErrorr{rqrrrrsrtrurlrrw)r}rvrlrrs @r" is_scool_filers << !(#9:;; 8  ggkk(D) + .D9D99 @A  !&&("s1W:??+<'='AwZ__.%E%aj&78$  %      sAD AD /D 9D  Dctj|std|dgfd}tj|d5}|d|t ||dddt S#1swYt SxYw)z List group paths to all cooler data collections in a file. Parameters ---------- filepath : str Returns ------- list Cooler group paths in the file. rrclt|r(j|jdsd|zn|yyNrFrwappend startswithpthrnlistings r" _check_coolerz#list_coolers.._check_cooler, c? NNCNN3,?39S I r$rrFN)ryrzrr{rcrr}rrrs @r"rrs << !(#9:;;GJ 8S !%Qc11m$% W  % W s A,,A?cfd}t|rVgtj|d5}|d|t||ddddvrj dt St d|d#1swY8xYw)z List the paths to all single-cell cool matrices in a file scool file. Parameters ---------- filepath : str Returns ------- list Cooler group paths of all cells in the file. clt|r(j|jdsd|zn|yyrrrs r"rz'list_scool_cells.._check_coolerrr$rrFNrz' is not a scool file.)rryr{rcremoverrrs @r"list_scool_cellsrsJX YYx % ) #q ! q- ( ) '> NN3 !!(#9:;; ) )s A77Bct|\}}tj|std|dgfd}tj|d5}|||t |||dddS#1swYSxYw)z Get all groups and datasets in an HDF5 file. Parameters ---------- uri : str Returns ------- list Group and dataset paths. rrc^j|jds d|zy|yr)rrrs r" _check_allzls.._check_all s#s(;sSyEEr$rN)rryrzrr{rc)r|r}r~rrrs @r"lsrs+3/Hi << !(#9:;;GF 8S !-Q9a 1Y<,- N - Ns A44A>cTt|\}}t|\}} t|||gdkDr tdtjj |r|rd} nd} ||k(rd} nd} t j|| 5} t j|| 5} ||k(r@|s|r| || | <|r| |=n|rt j|| | <n| j|| n|r td|rt j||| | <n|| dk(r]| |jD]}| j|dz|z| || | jj| |jn| j|| | dk7r| ndddddddy#1swYxYw#1swYyxYw)Nr z:Must provide at most one of: "link", "rename", "soft_link"wzr+rz,Can't hard link between two different files.rF)rsumr0ospathisfileryr{SoftLinkcopyr ExternalLinkrlrqupdate)src_uridst_uri overwritelinkrename soft_linksrc_path src_groupdst_path dst_groupdst_write_modesrc_write_modesrcdstsubgrps r"_copyrs+73Hi*73Hi D&) $%)UVV 77>>( #y8 8^ ,V 8^ ,V03 x v!$YII!%y!9II.LMM!%!2!28Y!GI#"%i."5"5"7HS6!93GH N((//I0D0DEHHY)s:JYPTU-VVVVVVs%?FC+FFF FF'c&t|||dddy)zICopy a group or dataset from one file to another or within the same file.FrrrNrrrrs r"rrEs '7IE%5Qr$c&t|||dddy)z/Rename a group or dataset within the same file.FTrNrrs r"rrJs '7IE$%Pr$c(t|||| d|y)zCreate a hard link to a group or dataset in the same file. Also supports soft links (in the same file) or external links (different files). FrNr)rrsoftrs r"rrOs  '7IHUdSr$c ddl dd d d fd j}t||}|j |d||S#t$r}t|ddd}~wwxYw) Nrz: Run `pip install ipytree` or `conda install ipytree`to get the required ipytree dependency for displaying the tree widget. If using jupyterlab, you also need to run `jupyter labextension install ipytree`c2|dvry|dvrytd|)N>ArrayDatasettable>r{GroupfolderzUnknown type: )r0)stypes r"_tree_get_iconz#tree_widget.._tree_get_iconfs. 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