{
"cells": [
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
"import ipyigv as igv\n",
"from ipywidgets.widgets.trait_types import InstanceDict\n",
"from ipyigv.options import ReferenceGenome, Track\n",
"from ipywidgets import Output "
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Initializing the browser "
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [],
"source": [
"genomeDict=igv.PUBLIC_GENOMES.hg38"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [],
"source": [
"genome = ReferenceGenome(**genomeDict)"
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [],
"source": [
"browser = igv.IgvBrowser(genome=genome)"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "72046f0dd69f4344a5704ee1d5464f1a",
"version_major": 2,
"version_minor": 0
},
"text/plain": [
"IgvBrowser(genome=ReferenceGenome(cytobandURL='https://s3.dualstack.us-east-1.amazonaws.com/igv.org.genomes/hg…"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"browser"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Adding or removing a track"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [],
"source": [
"trackDict = {'name': 'Refseq Genes',\n",
" 'format': 'refgene',\n",
" 'url': 'https://s3.dualstack.us-east-1.amazonaws.com/igv.org.genomes/hg38/refGene.txt.gz',\n",
" 'indexed': False,\n",
" 'visibilityWindow': -1,\n",
" 'removable': False,\n",
" 'order': 1000000}"
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [],
"source": [
"oneMoreTrack = Track(**trackDict)"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [],
"source": [
"browser.add_track(oneMoreTrack)"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [],
"source": [
"browser.remove_track(oneMoreTrack)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Adding a Region of Interest"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {},
"outputs": [],
"source": [
"roiDict = {\n",
" 'name': 'ROI set 1',\n",
" 'url': 'https://s3.amazonaws.com/igv.org.test/data/roi/roi_bed_1.bed',\n",
" 'indexed': False,\n",
" 'color': \"rgba(68, 134, 247, 0.25)\"\n",
"}"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {},
"outputs": [],
"source": [
"roi=igv.options.AnnotationTrack(**roiDict)"
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {},
"outputs": [],
"source": [
"browser.add_roi(roi)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Searching"
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"search\n"
]
}
],
"source": [
"browser.search('chr3:1-190,100,300')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Getting the browser configuration\n",
"We need to output the configuration in `browser.out`, which is an `Output` widget"
]
},
{
"cell_type": "code",
"execution_count": 17,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Dumping JSON to browser.out\n"
]
}
],
"source": [
"browser.dump_json()"
]
},
{
"cell_type": "code",
"execution_count": 18,
"metadata": {
"scrolled": true
},
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "9a164e5ec14b4b95b1b8257b3f6499ad",
"version_major": 2,
"version_minor": 0
},
"text/plain": [
"Output(outputs=({'output_type': 'stream', 'text': \"{'version': '2.7.0', 'reference': {'id': 'hg38', 'name': 'H…"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"browser.out"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Charging local files\n",
"NB: `igv.js` tries to load a file `undefined.fai` which causes an error. Maybe due to the use of `localhost:8000` -- activate it with `python -m http.server` in your files directory."
]
},
{
"cell_type": "code",
"execution_count": 19,
"metadata": {},
"outputs": [],
"source": [
"genome2 = {\n",
" 'name': 'Example chr6p',\n",
" 'fastaURL': 'http://localhost:8000/chr6p.fa',\n",
" 'indexURL': 'http://localhost:8000/chr6p.fa.fai',\n",
"}"
]
},
{
"cell_type": "code",
"execution_count": 20,
"metadata": {},
"outputs": [],
"source": [
"pgf6p_on_chr6p_track = {'name': 'PGF 6p on chr6p',\n",
" 'format': 'refgene',\n",
" 'url': 'http://localhost:8000/PGF_6p_on_chr6p.bam',\n",
" 'indexURL': 'http://localhost:8000/PGF_6p_on_chr6p.bai',\n",
" }"
]
},
{
"cell_type": "code",
"execution_count": 21,
"metadata": {},
"outputs": [],
"source": [
"browser2 = igv.IgvBrowser(genome=ReferenceGenome(**genome2))"
]
},
{
"cell_type": "code",
"execution_count": 22,
"metadata": {},
"outputs": [
{
"data": {
"application/vnd.jupyter.widget-view+json": {
"model_id": "08c6dcc3894843c290738b319e53c84b",
"version_major": 2,
"version_minor": 0
},
"text/plain": [
"IgvBrowser(genome=ReferenceGenome(fastaURL='http://localhost:8000/chr6p.fa', indexURL='http://localhost:8000/c…"
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"browser2"
]
},
{
"cell_type": "code",
"execution_count": 23,
"metadata": {},
"outputs": [],
"source": [
"import urllib.request"
]
},
{
"cell_type": "code",
"execution_count": 24,
"metadata": {},
"outputs": [
{
"ename": "URLError",
"evalue": "<urlopen error [Errno 61] Connection refused>",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mConnectionRefusedError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m~/opt/miniconda3/envs/widgets/lib/python3.9/urllib/request.py\u001b[0m in \u001b[0;36mdo_open\u001b[0;34m(self, http_class, req, **http_conn_args)\u001b[0m\n\u001b[1;32m 1341\u001b[0m \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1342\u001b[0;31m h.request(req.get_method(), req.selector, req.data, headers,\n\u001b[0m\u001b[1;32m 1343\u001b[0m encode_chunked=req.has_header('Transfer-encoding'))\n",
"\u001b[0;32m~/opt/miniconda3/envs/widgets/lib/python3.9/http/client.py\u001b[0m in \u001b[0;36mrequest\u001b[0;34m(self, method, url, body, headers, encode_chunked)\u001b[0m\n\u001b[1;32m 1254\u001b[0m \u001b[0;34m\"\"\"Send a complete request to the server.\"\"\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1255\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_send_request\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmethod\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0murl\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mbody\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mheaders\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mencode_chunked\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1256\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/opt/miniconda3/envs/widgets/lib/python3.9/http/client.py\u001b[0m in \u001b[0;36m_send_request\u001b[0;34m(self, method, url, body, headers, encode_chunked)\u001b[0m\n\u001b[1;32m 1300\u001b[0m \u001b[0mbody\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0m_encode\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mbody\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'body'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1301\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mendheaders\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mbody\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mencode_chunked\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mencode_chunked\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1302\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/opt/miniconda3/envs/widgets/lib/python3.9/http/client.py\u001b[0m in \u001b[0;36mendheaders\u001b[0;34m(self, message_body, encode_chunked)\u001b[0m\n\u001b[1;32m 1249\u001b[0m \u001b[0;32mraise\u001b[0m \u001b[0mCannotSendHeader\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1250\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_send_output\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmessage_body\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mencode_chunked\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mencode_chunked\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1251\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/opt/miniconda3/envs/widgets/lib/python3.9/http/client.py\u001b[0m in \u001b[0;36m_send_output\u001b[0;34m(self, message_body, encode_chunked)\u001b[0m\n\u001b[1;32m 1009\u001b[0m \u001b[0;32mdel\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_buffer\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1010\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msend\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1011\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/opt/miniconda3/envs/widgets/lib/python3.9/http/client.py\u001b[0m in \u001b[0;36msend\u001b[0;34m(self, data)\u001b[0m\n\u001b[1;32m 949\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mauto_open\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 950\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mconnect\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 951\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/opt/miniconda3/envs/widgets/lib/python3.9/http/client.py\u001b[0m in \u001b[0;36mconnect\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 920\u001b[0m \u001b[0;34m\"\"\"Connect to the host and port specified in __init__.\"\"\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 921\u001b[0;31m self.sock = self._create_connection(\n\u001b[0m\u001b[1;32m 922\u001b[0m (self.host,self.port), self.timeout, self.source_address)\n",
"\u001b[0;32m~/opt/miniconda3/envs/widgets/lib/python3.9/socket.py\u001b[0m in \u001b[0;36mcreate_connection\u001b[0;34m(address, timeout, source_address)\u001b[0m\n\u001b[1;32m 842\u001b[0m \u001b[0;32mtry\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 843\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0merr\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 844\u001b[0m \u001b[0;32mfinally\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/opt/miniconda3/envs/widgets/lib/python3.9/socket.py\u001b[0m in \u001b[0;36mcreate_connection\u001b[0;34m(address, timeout, source_address)\u001b[0m\n\u001b[1;32m 830\u001b[0m \u001b[0msock\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mbind\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0msource_address\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 831\u001b[0;31m \u001b[0msock\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mconnect\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0msa\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 832\u001b[0m \u001b[0;31m# Break explicitly a reference cycle\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mConnectionRefusedError\u001b[0m: [Errno 61] Connection refused",
"\nDuring handling of the above exception, another exception occurred:\n",
"\u001b[0;31mURLError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-24-0ba9ddfa92c7>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0murl\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0murllib\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrequest\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0murlopen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'http://localhost:8000/chr6p.fa.fai'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;32m~/opt/miniconda3/envs/widgets/lib/python3.9/urllib/request.py\u001b[0m in \u001b[0;36murlopen\u001b[0;34m(url, data, timeout, cafile, capath, cadefault, context)\u001b[0m\n\u001b[1;32m 212\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 213\u001b[0m \u001b[0mopener\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0m_opener\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 214\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mopener\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mopen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0murl\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdata\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mtimeout\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 215\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 216\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0minstall_opener\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mopener\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/opt/miniconda3/envs/widgets/lib/python3.9/urllib/request.py\u001b[0m in \u001b[0;36mopen\u001b[0;34m(self, fullurl, data, timeout)\u001b[0m\n\u001b[1;32m 515\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 516\u001b[0m \u001b[0msys\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0maudit\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'urllib.Request'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mreq\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfull_url\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mreq\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdata\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mreq\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mheaders\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mreq\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget_method\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 517\u001b[0;31m \u001b[0mresponse\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0m_open\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mreq\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdata\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 518\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 519\u001b[0m \u001b[0;31m# post-process response\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/opt/miniconda3/envs/widgets/lib/python3.9/urllib/request.py\u001b[0m in \u001b[0;36m_open\u001b[0;34m(self, req, data)\u001b[0m\n\u001b[1;32m 532\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 533\u001b[0m \u001b[0mprotocol\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mreq\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mtype\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 534\u001b[0;31m result = self._call_chain(self.handle_open, protocol, protocol +\n\u001b[0m\u001b[1;32m 535\u001b[0m '_open', req)\n\u001b[1;32m 536\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mresult\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/opt/miniconda3/envs/widgets/lib/python3.9/urllib/request.py\u001b[0m in \u001b[0;36m_call_chain\u001b[0;34m(self, chain, kind, meth_name, *args)\u001b[0m\n\u001b[1;32m 492\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mhandler\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mhandlers\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 493\u001b[0m \u001b[0mfunc\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mgetattr\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mhandler\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmeth_name\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 494\u001b[0;31m \u001b[0mresult\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mfunc\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m*\u001b[0m\u001b[0margs\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 495\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mresult\u001b[0m \u001b[0;32mis\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 496\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0mresult\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/opt/miniconda3/envs/widgets/lib/python3.9/urllib/request.py\u001b[0m in \u001b[0;36mhttp_open\u001b[0;34m(self, req)\u001b[0m\n\u001b[1;32m 1369\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1370\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mhttp_open\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mreq\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1371\u001b[0;31m \u001b[0;32mreturn\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdo_open\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mhttp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mclient\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mHTTPConnection\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mreq\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1372\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1373\u001b[0m \u001b[0mhttp_request\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mAbstractHTTPHandler\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdo_request_\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/opt/miniconda3/envs/widgets/lib/python3.9/urllib/request.py\u001b[0m in \u001b[0;36mdo_open\u001b[0;34m(self, http_class, req, **http_conn_args)\u001b[0m\n\u001b[1;32m 1343\u001b[0m encode_chunked=req.has_header('Transfer-encoding'))\n\u001b[1;32m 1344\u001b[0m \u001b[0;32mexcept\u001b[0m \u001b[0mOSError\u001b[0m \u001b[0;32mas\u001b[0m \u001b[0merr\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0;31m# timeout error\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1345\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mURLError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0merr\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1346\u001b[0m \u001b[0mr\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mh\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mgetresponse\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1347\u001b[0m \u001b[0;32mexcept\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mURLError\u001b[0m: <urlopen error [Errno 61] Connection refused>"
]
}
],
"source": [
"url = urllib.request.urlopen('http://localhost:8000/chr6p.fa.fai')"
]
},
{
"cell_type": "code",
"execution_count": 25,
"metadata": {},
"outputs": [
{
"ename": "NameError",
"evalue": "name 'url' is not defined",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-25-c0f5215b53c0>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0murl\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mread\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;36m100\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mdecode\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'utf-8'\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;31mNameError\u001b[0m: name 'url' is not defined"
]
}
],
"source": [
"print(url.read(100).decode('utf-8'))"
]
},
{
"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": "3.9.0"
}
},
"nbformat": 4,
"nbformat_minor": 4
}