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chore: Pin minimum Python version; Upgrade Ruff (#174)
* Add `requires-python` to `pyproject.toml` * Cleanup hatchling build config * Update ruff version * Apply Ruff formatting
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‎.python-version‎

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‎examples/Examples.ipynb‎

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{
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"cell_type": "code",
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"execution_count": null,
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"id": "cfdd679e",
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"metadata": {},
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"outputs": [],
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "37383869",
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"metadata": {},
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"outputs": [],
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},
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{
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"cell_type": "markdown",
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"id": "f5a73851",
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"metadata": {},
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"source": [
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"## Synced heatmaps"
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "ba0c9d3e",
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"metadata": {},
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"outputs": [],
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"source": [
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "4b6c2629",
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"metadata": {},
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"outputs": [],
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"source": [
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "1453f49f",
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"metadata": {},
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"outputs": [],
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"source": [
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "4432d5d1",
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"metadata": {},
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"outputs": [],
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},
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{
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"cell_type": "markdown",
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"id": "637bcad2",
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"metadata": {},
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"source": [
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"## Value scale syncing"
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "e89a03d7",
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"metadata": {},
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"outputs": [],
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"source": [
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"# Creates a hg.RemoteTileset object\n",
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"remote_tileset = hg.remote(\n",
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" uid=\"CQMd6V_cRw6iCI_-Unl3PQ\",\n",
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" server=\"https://higlass.io/api/v1/\", # optional, \"http://higlass.io/api/v1/\" default\n",
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" server=\"https://higlass.io/api/v1/\", # optional, \"http://higlass.io/api/v1/\"\n",
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" name=\"Rao et al. (2014) GM12878 MboI (allreps) 1kb\",\n",
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")\n",
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"\n",
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},
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{
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"cell_type": "markdown",
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"id": "ef880b6c",
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"metadata": {},
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"source": [
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"## Remote heatmaps"
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{
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"cell_type": "code",
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"id": "4579c459",
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"metadata": {},
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"outputs": [],
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},
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{
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"cell_type": "markdown",
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"id": "74b22d9c",
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"metadata": {},
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"source": [
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"## Extract track from another view config"
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{
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"cell_type": "code",
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"id": "875260a4",
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"metadata": {},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "f22d06ae",
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"metadata": {},
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"outputs": [],
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"source": [
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "73c925a5",
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"metadata": {},
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"outputs": [],
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},
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{
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"cell_type": "markdown",
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"id": "0a9ad2fc",
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"metadata": {},
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"source": [
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"## Remote bigWig tiles\n",
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{
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"cell_type": "code",
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"id": "3d664bb6",
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"metadata": {},
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"source": [
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "0e22f81d",
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"metadata": {},
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"outputs": [],
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"source": [
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "4133c1c3",
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"metadata": {},
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"outputs": [],
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"source": [
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"import hg\n",
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"\n",
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"# get mounted path\n",
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"bwpath = hg.fuse.path(\n",
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" f\"http://hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/\"\n",
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" f\"wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878InputStdSig.bigWig\"\n",
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" \"http://hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/\"\n",
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" \"wgEncodeSydhTfbs/wgEncodeSydhTfbsGm12878InputStdSig.bigWig\"\n",
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")\n",
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"\n",
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"track = hg.bigwig(bwpath).track(\"horizontal-bar\")\n",
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},
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"cell_type": "markdown",
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"metadata": {
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"tags": []
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},
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"id": "5844a303",
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"metadata": {},
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"source": [
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"## Local cooler files\n",
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"\n",
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "0439622f",
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"metadata": {},
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"outputs": [],
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"source": [
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"tileset = hg.cooler(\"../test/data/Dixon2012-J1-NcoI-R1-filtered.100kb.multires.cool\")\n",
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"hg.view(tileset.track(\"heatmap\"))"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Local bigWig files (with chromsizes)\n",
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"\n",
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"### TODO: inline `chromsizes` tilesets are not yet implemented"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"chromsizes = [\n",
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" (\"chr1\", 249250621),\n",
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" (\"chr2\", 243199373),\n",
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" (\"chr3\", 198022430),\n",
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" (\"chr4\", 191154276),\n",
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" (\"chr5\", 180915260),\n",
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" (\"chr6\", 171115067),\n",
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" (\"chr7\", 159138663),\n",
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" (\"chr8\", 146364022),\n",
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" (\"chr9\", 141213431),\n",
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" (\"chr10\", 135534747),\n",
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" (\"chr11\", 135006516),\n",
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" (\"chr12\", 133851895),\n",
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" (\"chr13\", 115169878),\n",
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" (\"chr14\", 107349540),\n",
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" (\"chr15\", 102531392),\n",
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" (\"chr16\", 90354753),\n",
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" (\"chr17\", 81195210),\n",
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" (\"chr18\", 78077248),\n",
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" (\"chr20\", 63025520),\n",
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" (\"chr19\", 59128983),\n",
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" (\"chr21\", 48129895),\n",
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" (\"chr22\", 51304566),\n",
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" (\"chrX\", 155270560),\n",
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" (\"chrY\", 59373566),\n",
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" (\"chrM\", 16571),\n",
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"]\n",
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"\n",
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"bigwig_fp = (\n",
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" \"../test/data/wgEncodeCaltechRnaSeqHuvecR1x75dTh1014IlnaPlusSignalRep2.bigWig\"\n",
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")\n",
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"ts = hg.bigwig(bigwig_fp, chromsizes=chromsizes)\n",
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"cs = hg.ChromSizes(chromsizes)\n",
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"\n",
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"view1 = View(\n",
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" [\n",
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" Track(\"top-axis\"),\n",
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" Track(\"horizontal-bar\", tileset=ts),\n",
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" Track(\"horizontal-chromosome-labels\", position=\"top\", tileset=cs),\n",
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" ]\n",
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")\n",
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"display, server, viewconf = higlass.display([view1])\n",
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"\n",
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"display"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Local bedlike data\n",
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"\n",
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"### TODO: inline `bedlike` tilesets are not yet implemented"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"import hg\n",
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"\n",
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"bed = [\n",
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" [\"chr1\", 1000, 2000, \"item #1\", \".\", \"+\"],\n",
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" [\"chr2\", 3000, 3500, \"item #1\", \".\", \"-\"],\n",
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"]\n",
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"\n",
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"chroms = [\n",
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" [\"chr1\", 2100],\n",
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" [\"chr2\", 4000],\n",
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"]\n",
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"\n",
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"\n",
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"data = bedtiles(bed, chroms)\n",
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"track = Track(\n",
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" track_type=\"bedlike\",\n",
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" position=\"top\",\n",
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" height=50,\n",
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" data=data,\n",
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" options={\"minusStrandColor\": \"red\"},\n",
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")\n",
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"\n",
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"\n",
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"d, s, v = higlass.display([[track]])\n",
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"d"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Custom data"
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]
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"import numpy as np\n",
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"\n",
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"dim = 2000\n",
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"I, J = np.indices((dim, dim))\n",
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"data = -(J + 47) * np.sin(np.sqrt(np.abs(I / 2 + (J + 47)))) - I * np.sin(\n",
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" np.sqrt(np.abs(I - (J + 47)))\n",
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")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"import clodius.tiles.npmatrix\n",
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"from hg.tilesets import LocalTileset\n",
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"\n",
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"ts = hg.server.add(\n",
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" LocalTileset(\n",
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" uid=\"my-custom-tileset\",\n",
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" info=lambda: clodius.tiles.npmatrix.tileset_info(data),\n",
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" tiles=lambda tids: clodius.tiles.npmatrix.tiles_wrapper(data, tids),\n",
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" )\n",
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")\n",
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"\n",
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"hg.view(\n",
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" (hg.track(\"top-axis\"), \"top\"),\n",
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" (hg.track(\"left-axis\"), \"left\"),\n",
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" (ts.track(\"heatmap\", height=250).opts(valueScaleMax=0.5), \"center\"),\n",
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")"
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]
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},
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"outputs": [],
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"source": []
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}
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],
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"metadata": {

‎examples/JupyterServer.ipynb‎

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"import higlass as hg\n",
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"ts = hg.cooler(\"./test.mcool\") # local tileset\n",
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"ts = hg.cooler(\"./test.mcool\") # local tileset\n",
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"hg.view(ts.track(\"heatmap\"), width=6)"
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