Created
March 4, 2016 07:19
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{ | |
"cells": [ | |
{ | |
"cell_type": "code", | |
"execution_count": 1, | |
"metadata": { | |
"collapsed": true | |
}, | |
"outputs": [], | |
"source": [ | |
"from biomart import BiomartServer" | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": 2, | |
"metadata": { | |
"collapsed": false | |
}, | |
"outputs": [], | |
"source": [ | |
"server = BiomartServer('http://www.ensembl.org/biomart')" | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": 3, | |
"metadata": { | |
"collapsed": false | |
}, | |
"outputs": [ | |
{ | |
"ename": "HTTPError", | |
"evalue": "404 Client Error: Not Found for url: http://www.biomart.org/biomart/martservice", | |
"output_type": "error", | |
"traceback": [ | |
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", | |
"\u001b[0;31mHTTPError\u001b[0m Traceback (most recent call last)", | |
"\u001b[0;32m<ipython-input-3-2d5fd97db923>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mserver\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mBiomartServer\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/somewhere/site-packages/biomart-0.8.0-py3.5.egg/biomart/server.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, url, **kwargs)\u001b[0m\n\u001b[1;32m 25\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 26\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mis_alive\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mFalse\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 27\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0massert_alive\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 28\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 29\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mget_verbose\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", | |
"\u001b[0;32m/somewhere/site-packages/biomart-0.8.0-py3.5.egg/biomart/server.py\u001b[0m in \u001b[0;36massert_alive\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 46\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0massert_alive\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 47\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0;32mnot\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mis_alive\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 48\u001b[0;31m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget_request\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 49\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mis_alive\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;32mTrue\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 50\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mverbose\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", | |
"\u001b[0;32m/somewhere/site-packages/biomart-0.8.0-py3.5.egg/biomart/server.py\u001b[0m in \u001b[0;36mget_request\u001b[0;34m(self, **params)\u001b[0m\n\u001b[1;32m 102\u001b[0m \u001b[0;32melse\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 103\u001b[0m \u001b[0mr\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mrequests\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0murl\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mproxies\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mproxies\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 104\u001b[0;31m \u001b[0mr\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mraise_for_status\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 105\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 106\u001b[0m \u001b[0;32mreturn\u001b[0m \u001b[0mr\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", | |
"\u001b[0;32m/somewhere/site-packages/requests/models.py\u001b[0m in \u001b[0;36mraise_for_status\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 838\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 839\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mhttp_error_msg\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 840\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mHTTPError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mhttp_error_msg\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mresponse\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 841\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 842\u001b[0m \u001b[0;32mdef\u001b[0m \u001b[0mclose\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n", | |
"\u001b[0;31mHTTPError\u001b[0m: 404 Client Error: Not Found for url: http://www.biomart.org/biomart/martservice" | |
] | |
} | |
], | |
"source": [ | |
"server = BiomartServer()" | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": null, | |
"metadata": { | |
"collapsed": true | |
}, | |
"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": "3.5.1" | |
} | |
}, | |
"nbformat": 4, | |
"nbformat_minor": 0 | |
} |
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