notebook.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "%load_ext autoreload\n",
    "%autoreload 2"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {},
   "outputs": [],
   "source": [
    "tads = \"\"\"chr1    1760000 2640000\n",
    "chr1    2640000 2760000\n",
    "chr1    2760000 5960000\n",
    "chr1    5960000 6440000\n",
    "chr1    6440000 7960000\n",
    "chr1    7960000 8360000\n",
    "chr1    8360000 8880000\n",
    "chr1    8880000 9600000\n",
    "chr1    9600000 10160000\n",
    "chr1    10160000        10440000\"\"\"\n",
    "\n",
    "with open('/tmp/tads.bed', 'w') as f:\n",
    "    f.write(tads)\n",
    "    \n",
    "import subprocess as sp\n",
    "ret = sp.call(['clodius', 'aggregate', 'bedpe', '--chr1-col', '1', '--chr2-col', '1', \n",
    "               '--from1-col', '2', '--from2-col', '2',\n",
    "               '--to1-col', '3', '--to2-col', '3', '/tmp/tads.bed'])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 73,
   "metadata": {},
   "outputs": [],
   "source": [
    "from clodius.tiles.utils import tiles_wrapper_2d\n",
    "\n",
    "def bed2ddb(filepath, uuid=None, **kwargs):\n",
    "    from clodius.tiles.bed2ddb import get_2d_tileset_info, get_2D_tiles\n",
    "\n",
    "    return Tileset(\n",
    "        uuid=uuid,\n",
    "        tileset_info=lambda: get_2d_tileset_info(filepath),\n",
    "        tiles=lambda tids: tiles_wrapper_2d(\n",
    "            tids, lambda z, x, y: get_2D_tiles(filepath, z, x, y)[(x, y)]\n",
    "        ),\n",
    "        **kwargs\n",
    "    )"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 74,
   "metadata": {},
   "outputs": [],
   "source": [
    "import higlass.tilesets as ti\n",
    "\n",
    "ts = bed2ddb('/tmp/tads.bed.multires.db')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 78,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "application/vnd.jupyter.widget-view+json": {
       "model_id": "b09a92782ba74302a274ff03a5625c1c",
       "version_major": 2,
       "version_minor": 0
      },
      "text/plain": [
       "HiGlassDisplay(viewconf={'editable': True, 'views': [{'uid': 'IA9Xr33SQJCNpt_LbTu95w', 'tracks': {'top': [{'ty…"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "from higlass.client import Track, View\n",
    "import higlass\n",
    "\n",
    "(d,s,v) = higlass.display([\n",
    "    View([\n",
    "        Track('top-axis'),\n",
    "        Track('2d-rectangle-domains', position='center', tileset=ts, height=400)\n",
    "    ], initialXDomain=[0, 20e6])\n",
    "])\n",
    "d"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.6.2"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}