{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
"Collecting git+https://github.com/GMOD/jbrowse-jupyter.git@main\n",
" Cloning https://github.com/GMOD/jbrowse-jupyter.git (to revision main) to /private/var/folders/96/hq94_1qd3c9_q87bwqhg05s80000gn/T/pip-req-build-emfgm9s3\n",
" Running command git clone --filter=blob:none -q https://github.com/GMOD/jbrowse-jupyter.git /private/var/folders/96/hq94_1qd3c9_q87bwqhg05s80000gn/T/pip-req-build-emfgm9s3\n",
" Resolved https://github.com/GMOD/jbrowse-jupyter.git to commit 5a7a753cf3ada2d028992c67ed305e0ea575555b\n",
" Preparing metadata (setup.py) ... \u001b[?25ldone\n",
"\u001b[?25hCollecting dash==2.0.0\n",
" Using cached dash-2.0.0-py3-none-any.whl (7.3 MB)\n",
"Collecting dash-jbrowse>=1.0.1\n",
" Using cached dash_jbrowse-1.0.1-py3-none-any.whl (1.1 MB)\n",
"Requirement already satisfied: flake8>=4.0.1 in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from jbrowse-jupyter==1.2.1) (4.0.1)\n",
"Requirement already satisfied: jupyter_dash>=0.4.0 in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from jbrowse-jupyter==1.2.1) (0.4.0)\n",
"Requirement already satisfied: pandas>=1.1.5 in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from jbrowse-jupyter==1.2.1) (1.4.0)\n",
"Requirement already satisfied: pytest>=6.2.5 in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from jbrowse-jupyter==1.2.1) (6.2.5)\n",
"Requirement already satisfied: dash-table==5.0.0 in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from dash==2.0.0->jbrowse-jupyter==1.2.1) (5.0.0)\n",
"Requirement already satisfied: flask-compress in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from dash==2.0.0->jbrowse-jupyter==1.2.1) (1.10.1)\n",
"Requirement already satisfied: dash-core-components==2.0.0 in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from dash==2.0.0->jbrowse-jupyter==1.2.1) (2.0.0)\n",
"Requirement already satisfied: plotly>=5.0.0 in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from dash==2.0.0->jbrowse-jupyter==1.2.1) (5.3.1)\n",
"Requirement already satisfied: dash-html-components==2.0.0 in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from dash==2.0.0->jbrowse-jupyter==1.2.1) (2.0.0)\n",
"Requirement already satisfied: Flask>=1.0.4 in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from dash==2.0.0->jbrowse-jupyter==1.2.1) (1.1.2)\n",
"Requirement already satisfied: pycodestyle<2.9.0,>=2.8.0 in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from flake8>=4.0.1->jbrowse-jupyter==1.2.1) (2.8.0)\n",
"Requirement already satisfied: mccabe<0.7.0,>=0.6.0 in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from flake8>=4.0.1->jbrowse-jupyter==1.2.1) (0.6.1)\n",
"Requirement already satisfied: pyflakes<2.5.0,>=2.4.0 in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from flake8>=4.0.1->jbrowse-jupyter==1.2.1) (2.4.0)\n",
"Requirement already satisfied: ipykernel in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from jupyter_dash>=0.4.0->jbrowse-jupyter==1.2.1) (5.3.4)\n",
"Requirement already satisfied: ansi2html in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from jupyter_dash>=0.4.0->jbrowse-jupyter==1.2.1) (1.6.0)\n",
"Requirement already satisfied: retrying in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from jupyter_dash>=0.4.0->jbrowse-jupyter==1.2.1) (1.3.3)\n",
"Requirement already satisfied: requests in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from jupyter_dash>=0.4.0->jbrowse-jupyter==1.2.1) (2.24.0)\n",
"Requirement already satisfied: ipython in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from jupyter_dash>=0.4.0->jbrowse-jupyter==1.2.1) (7.19.0)\n",
"Requirement already satisfied: python-dateutil>=2.8.1 in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from pandas>=1.1.5->jbrowse-jupyter==1.2.1) (2.8.1)\n",
"Requirement already satisfied: numpy>=1.18.5 in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from pandas>=1.1.5->jbrowse-jupyter==1.2.1) (1.19.2)\n",
"Requirement already satisfied: pytz>=2020.1 in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from pandas>=1.1.5->jbrowse-jupyter==1.2.1) (2020.1)\n",
"Requirement already satisfied: packaging in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from pytest>=6.2.5->jbrowse-jupyter==1.2.1) (20.4)\n",
"Requirement already satisfied: iniconfig in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from pytest>=6.2.5->jbrowse-jupyter==1.2.1) (1.1.1)\n",
"Requirement already satisfied: attrs>=19.2.0 in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from pytest>=6.2.5->jbrowse-jupyter==1.2.1) (20.3.0)\n",
"Requirement already satisfied: py>=1.8.2 in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from pytest>=6.2.5->jbrowse-jupyter==1.2.1) (1.9.0)\n",
"Requirement already satisfied: toml in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from pytest>=6.2.5->jbrowse-jupyter==1.2.1) (0.10.1)\n",
"Requirement already satisfied: pluggy<2.0,>=0.12 in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from pytest>=6.2.5->jbrowse-jupyter==1.2.1) (0.13.1)\n",
"Requirement already satisfied: click>=5.1 in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from Flask>=1.0.4->dash==2.0.0->jbrowse-jupyter==1.2.1) (7.1.2)\n",
"Requirement already satisfied: itsdangerous>=0.24 in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from Flask>=1.0.4->dash==2.0.0->jbrowse-jupyter==1.2.1) (1.1.0)\n",
"Requirement already satisfied: Jinja2>=2.10.1 in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from Flask>=1.0.4->dash==2.0.0->jbrowse-jupyter==1.2.1) (2.11.2)\n",
"Requirement already satisfied: Werkzeug>=0.15 in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from Flask>=1.0.4->dash==2.0.0->jbrowse-jupyter==1.2.1) (2.0.2)\n",
"Requirement already satisfied: tenacity>=6.2.0 in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from plotly>=5.0.0->dash==2.0.0->jbrowse-jupyter==1.2.1) (8.0.1)\n",
"Requirement already satisfied: six in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from plotly>=5.0.0->dash==2.0.0->jbrowse-jupyter==1.2.1) (1.16.0)\n",
"Requirement already satisfied: brotli in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from flask-compress->dash==2.0.0->jbrowse-jupyter==1.2.1) (1.0.9)\n",
"Requirement already satisfied: appnope in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from ipykernel->jupyter_dash>=0.4.0->jbrowse-jupyter==1.2.1) (0.1.0)\n",
"Requirement already satisfied: tornado>=4.2 in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from ipykernel->jupyter_dash>=0.4.0->jbrowse-jupyter==1.2.1) (6.0.4)\n",
"Requirement already satisfied: jupyter-client in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from ipykernel->jupyter_dash>=0.4.0->jbrowse-jupyter==1.2.1) (6.1.7)\n",
"Requirement already satisfied: traitlets>=4.1.0 in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from ipykernel->jupyter_dash>=0.4.0->jbrowse-jupyter==1.2.1) (5.1.1)\n",
"Requirement already satisfied: pygments in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from ipython->jupyter_dash>=0.4.0->jbrowse-jupyter==1.2.1) (2.7.2)\n",
"Requirement already satisfied: decorator in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from ipython->jupyter_dash>=0.4.0->jbrowse-jupyter==1.2.1) (4.4.2)\n",
"Requirement already satisfied: setuptools>=18.5 in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from ipython->jupyter_dash>=0.4.0->jbrowse-jupyter==1.2.1) (59.2.0)\n",
"Requirement already satisfied: backcall in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from ipython->jupyter_dash>=0.4.0->jbrowse-jupyter==1.2.1) (0.2.0)\n",
"Requirement already satisfied: prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0 in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from ipython->jupyter_dash>=0.4.0->jbrowse-jupyter==1.2.1) (3.0.8)\n",
"Requirement already satisfied: jedi>=0.10 in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from ipython->jupyter_dash>=0.4.0->jbrowse-jupyter==1.2.1) (0.17.1)\n",
"Requirement already satisfied: pexpect>4.3 in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from ipython->jupyter_dash>=0.4.0->jbrowse-jupyter==1.2.1) (4.8.0)\n",
"Requirement already satisfied: pickleshare in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from ipython->jupyter_dash>=0.4.0->jbrowse-jupyter==1.2.1) (0.7.5)\n",
"Requirement already satisfied: pyparsing>=2.0.2 in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from packaging->pytest>=6.2.5->jbrowse-jupyter==1.2.1) (2.4.7)\n",
"Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from requests->jupyter_dash>=0.4.0->jbrowse-jupyter==1.2.1) (1.25.11)\n",
"Requirement already satisfied: idna<3,>=2.5 in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from requests->jupyter_dash>=0.4.0->jbrowse-jupyter==1.2.1) (2.10)\n",
"Requirement already satisfied: certifi>=2017.4.17 in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from requests->jupyter_dash>=0.4.0->jbrowse-jupyter==1.2.1) (2020.6.20)\n",
"Requirement already satisfied: chardet<4,>=3.0.2 in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from requests->jupyter_dash>=0.4.0->jbrowse-jupyter==1.2.1) (3.0.4)\n",
"Requirement already satisfied: parso<0.8.0,>=0.7.0 in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from jedi>=0.10->ipython->jupyter_dash>=0.4.0->jbrowse-jupyter==1.2.1) (0.7.0)\n",
"Requirement already satisfied: MarkupSafe>=0.23 in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from Jinja2>=2.10.1->Flask>=1.0.4->dash==2.0.0->jbrowse-jupyter==1.2.1) (2.0.1)\n",
"Requirement already satisfied: ptyprocess>=0.5 in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from pexpect>4.3->ipython->jupyter_dash>=0.4.0->jbrowse-jupyter==1.2.1) (0.6.0)\n",
"Requirement already satisfied: wcwidth in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0->ipython->jupyter_dash>=0.4.0->jbrowse-jupyter==1.2.1) (0.2.5)\n",
"Requirement already satisfied: pyzmq>=13 in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from jupyter-client->ipykernel->jupyter_dash>=0.4.0->jbrowse-jupyter==1.2.1) (19.0.2)\n",
"Requirement already satisfied: jupyter-core>=4.6.0 in /Users/teresamartinez/opt/anaconda3/lib/python3.8/site-packages (from jupyter-client->ipykernel->jupyter_dash>=0.4.0->jbrowse-jupyter==1.2.1) (4.6.3)\n",
"Building wheels for collected packages: jbrowse-jupyter\n",
" Building wheel for jbrowse-jupyter (setup.py) ... \u001b[?25ldone\n",
"\u001b[?25h Created wheel for jbrowse-jupyter: filename=jbrowse_jupyter-1.2.1-py3-none-any.whl size=23012 sha256=dc06962e969611682d804c0be04df525f0ddaf4de081e7ff81ca334a6ad8ef75\n",
" Stored in directory: /private/var/folders/96/hq94_1qd3c9_q87bwqhg05s80000gn/T/pip-ephem-wheel-cache-_0jqacx4/wheels/a5/b8/b6/451f32abe96728b448365b4289261b6a436d79dd1ace71c4f1\n",
"Successfully built jbrowse-jupyter\n",
"Installing collected packages: dash, dash-jbrowse, jbrowse-jupyter\n",
" Attempting uninstall: dash\n",
" Found existing installation: dash 2.1.0\n",
" Uninstalling dash-2.1.0:\n",
" Successfully uninstalled dash-2.1.0\n",
" Attempting uninstall: dash-jbrowse\n",
" Found existing installation: dash-jbrowse 1.0.0\n",
" Uninstalling dash-jbrowse-1.0.0:\n",
" Successfully uninstalled dash-jbrowse-1.0.0\n",
"Successfully installed dash-2.0.0 dash-jbrowse-1.0.1 jbrowse-jupyter-1.2.1\n",
"\u001b[33mWARNING: You are using pip version 21.3.1; however, version 22.0.3 is available.\n",
"You should consider upgrading via the '/Users/teresamartinez/opt/anaconda3/bin/python -m pip install --upgrade pip' command.\u001b[0m\n"
]
}
],
"source": [
"!pip install git+https://github.com/GMOD/jbrowse-jupyter.git@main"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"import pandas as pd\n",
"from jbrowse_jupyter import launch, create"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
"hg38 = create('LGV', genome='hg38')"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
" refName start end name\n0 10 100 175 feature1\n1 10 150 225 feature2\n2 10 200 275 feature3\n3 10 250 325 feature4\n"
]
}
],
"source": [
"data = {'refName':['10', '10', '10', '10'],\n",
" 'start':[100, 150, 200, 250],\n",
" 'end':[175, 225, 275, 325],\n",
" 'name':['feature1', 'feature2', 'feature3', 'feature4']}\n",
"\n",
"df = pd.DataFrame(data)\n",
"print(df)\n",
"hg38.add_df_track(df, 'track_name', track_id=\"df_track_id\", overwrite=True)"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [
{
"output_type": "display_data",
"data": {
"text/plain": "<IPython.lib.display.IFrame at 0x7fac089d0438>",
"text/html": "\n <iframe\n width=\"100%\"\n height=\"300\"\n src=\"http://127.0.0.1:3003/\"\n frameborder=\"0\"\n allowfullscreen\n ></iframe>\n "
},
"metadata": {}
}
],
"source": [
"hg38.set_location(\"10:100..350\")\n",
"hg38.set_default_session(['df_track_id'], False)\n",
"new_conf = hg38.get_config()\n",
"launch(new_conf, port=3003)"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [],
"source": [
"tracks = [\n",
" (\"https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/ncbi_refseq/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz\", \"gff-demo\"),\n",
" (\"https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/skbr3/SKBR3_Feb17_GRCh38.sorted.bam\", \"bam-demo\"),\n",
" (\"https://s3.amazonaws.com/jbrowse.org/genomes/hg19/skbr3/reads_lr_skbr3.fa_ngmlr-0.2.3_mapped.down.cram\", \"cram-demo\"),\n",
" (\"https://hgdownload.cse.ucsc.edu/goldenpath/hg38/phyloP100way/hg38.phyloP100way.bw\", \"bigwig-demo\"),\n",
" (\"https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz\", \"vcf-demo\"),\n",
" (\"https://jbrowse.org/genomes/GRCh38/repeats.bb\", \"bigbed\")\n",
"]\n",
"for track in tracks:\n",
" data = track[0]\n",
" track_id = track[1]\n",
" hg38.add_track(data, track_id=track_id)"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [
{
"output_type": "display_data",
"data": {
"text/plain": "<IPython.lib.display.IFrame at 0x7fabc80d3668>",
"text/html": "\n <iframe\n width=\"100%\"\n height=\"800\"\n src=\"http://127.0.0.1:8000/\"\n frameborder=\"0\"\n allowfullscreen\n ></iframe>\n "
},
"metadata": {}
}
],
"source": [
"# set theme\n",
"hg38.set_theme(\"#311b92\", \"#0097a7\", \"#f57c00\", \"#d50000\")\n",
"hg38.set_default_session(['gff-demo', 'bigbed'],False)\n",
"hg38.set_location(\"1:110654228..110936130\")\n",
"new_conf2 = hg38.get_config()\n",
"launch(new_conf2, id=\"test-2\",height=800, dash_comp=\"LGV\", port=8000)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"name": "python3",
"display_name": "Python 3.6.13 64-bit ('penv': conda)",
"metadata": {
"interpreter": {
"hash": "008c12275884433fb16330e243da39c752250b643962dc839102136cfd0533c7"
}
}
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.13-final"
}
},
"nbformat": 4,
"nbformat_minor": 4
}