{ "cells": [ { "cell_type": "code", "execution_count": 1, "metadata": { "collapsed": false }, "outputs": [], "source": [ "from collections import defaultdict\n", "\n", "import requests\n", "\n", "from Bio import ExPASy, SwissProt" ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "collapsed": false }, "outputs": [], "source": [ "#explain why not biopython\n", "server = 'http://www.uniprot.org/uniprot'\n", "def do_request(server, ID='', **kwargs):\n", " params = ''\n", " req = requests.get('%s/%s%s' % (server, ID, params),params=kwargs)\n", " if not req.ok:\n", " req.raise_for_status()\n", " return req" ] }, { "cell_type": "code", "execution_count": 3, "metadata": { "collapsed": false }, "outputs": [], "source": [ "req = do_request(server, query='gene:p53 AND reviewed:yes',# AND organism:Human',\n", " format='tab',\n", " columns='id,entry name,length,organism,organism-id,database(PDB),database(HGNC)',\n", " limit='50')\n", "#We might revisit this for KEGG" ] }, { "cell_type": "code", "execution_count": 4, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/html": [ "
\n", " | Entry | \n", "Entry name | \n", "Length | \n", "Organism | \n", "ID | \n", "Cross-reference (PDB) | \n", "Cross-reference (HGNC) | \n", "
---|---|---|---|---|---|---|---|
0 | \n", "Q9W678 | \n", "P53_BARBU | \n", "369 | \n", "Barbus barbus (Barbel) (Cyprinus barbus) | \n", "40830 | \n", "NaN | \n", "NaN | \n", "
1 | \n", "Q29537 | \n", "P53_CANFA | \n", "381 | \n", "Canis familiaris (Dog) (Canis lupus familiaris) | \n", "9615 | \n", "NaN | \n", "NaN | \n", "
2 | \n", "O09185 | \n", "P53_CRIGR | \n", "393 | \n", "Cricetulus griseus (Chinese hamster) (Cricetul... | \n", "10029 | \n", "NaN | \n", "NaN | \n", "
3 | \n", "Q8SPZ3 | \n", "P53_DELLE | \n", "387 | \n", "Delphinapterus leucas (Beluga whale) | \n", "9749 | \n", "NaN | \n", "NaN | \n", "
4 | \n", "P79892 | \n", "P53_HORSE | \n", "280 | \n", "Equus caballus (Horse) | \n", "9796 | \n", "NaN | \n", "NaN | \n", "
5 | \n", "P04637 | \n", "P53_HUMAN | \n", "393 | \n", "Homo sapiens (Human) | \n", "9606 | \n", "1A1U;1AIE;1C26;1DT7;1GZH;1H26;1HS5;1JSP;1KZY;1... | \n", "11998; | \n", "
6 | \n", "O93379 | \n", "P53_ICTPU | \n", "376 | \n", "Ictalurus punctatus (Channel catfish) (Silurus... | \n", "7998 | \n", "NaN | \n", "NaN | \n", "
7 | \n", "P56423 | \n", "P53_MACFA | \n", "393 | \n", "Macaca fascicularis (Crab-eating macaque) (Cyn... | \n", "9541 | \n", "NaN | \n", "NaN | \n", "
8 | \n", "P61260 | \n", "P53_MACFU | \n", "393 | \n", "Macaca fuscata fuscata (Japanese macaque) | \n", "9543 | \n", "NaN | \n", "NaN | \n", "
9 | \n", "P56424 | \n", "P53_MACMU | \n", "393 | \n", "Macaca mulatta (Rhesus macaque) | \n", "9544 | \n", "NaN | \n", "NaN | \n", "
10 | \n", "P02340 | \n", "P53_MOUSE | \n", "387 | \n", "Mus musculus (Mouse) | \n", "10090 | \n", "1HU8;2GEQ;2IOI;2IOM;2IOO;2P52;3EXJ;3EXL; | \n", "NaN | \n", "
11 | \n", "P25035 | \n", "P53_ONCMY | \n", "396 | \n", "Oncorhynchus mykiss (Rainbow trout) (Salmo gai... | \n", "8022 | \n", "NaN | \n", "NaN | \n", "
12 | \n", "P79820 | \n", "P53_ORYLA | \n", "352 | \n", "Oryzias latipes (Medaka fish) (Japanese ricefish) | \n", "8090 | \n", "NaN | \n", "NaN | \n", "
13 | \n", "Q9TUB2 | \n", "P53_PIG | \n", "386 | \n", "Sus scrofa (Pig) | \n", "9823 | \n", "NaN | \n", "NaN | \n", "
14 | \n", "O12946 | \n", "P53_PLAFE | \n", "366 | \n", "Platichthys flesus (European flounder) (Pleuro... | \n", "8260 | \n", "NaN | \n", "NaN | \n", "
15 | \n", "P10361 | \n", "P53_RAT | \n", "391 | \n", "Rattus norvegicus (Rat) | \n", "10116 | \n", "NaN | \n", "NaN | \n", "
16 | \n", "Q9W679 | \n", "P53_TETMU | \n", "367 | \n", "Tetraodon miurus (Congo puffer) | \n", "94908 | \n", "NaN | \n", "NaN | \n", "
17 | \n", "Q9TTA1 | \n", "P53_TUPBE | \n", "393 | \n", "Tupaia belangeri (Common tree shrew) (Tupaia g... | \n", "37347 | \n", "NaN | \n", "NaN | \n", "
18 | \n", "O57538 | \n", "P53_XIPHE | \n", "342 | \n", "Xiphophorus helleri (Green swordtail) | \n", "8084 | \n", "NaN | \n", "NaN | \n", "
19 | \n", "Q92143 | \n", "P53_XIPMA | \n", "342 | \n", "Xiphophorus maculatus (Southern platyfish) (Pl... | \n", "8083 | \n", "NaN | \n", "NaN | \n", "
20 | \n", "Q42578 | \n", "PER53_ARATH | \n", "335 | \n", "Arabidopsis thaliana (Mouse-ear cress) | \n", "3702 | \n", "1PA2;1QO4; | \n", "NaN | \n", "