Created
May 15, 2016 18:11
-
-
Save rohanjaswal2507/16cd78d5684de859a9d9f23e394fad81 to your computer and use it in GitHub Desktop.
Simple jupyter widget to parse urls with clustal
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
{ | |
"cells": [ | |
{ | |
"cell_type": "code", | |
"execution_count": 1, | |
"metadata": { | |
"collapsed": false | |
}, | |
"outputs": [], | |
"source": [ | |
"import ipywidgets as widgets\n", | |
"from traitlets import Unicode, List\n", | |
"from IPython.display import display\n", | |
"\n", | |
"class MsaParseUrl(widgets.DOMWidget):\n", | |
" _view_name = Unicode('MsaParseUrlView').tag(sync=True)\n", | |
" _view_module = Unicode('MsaParseURL').tag(sync=True)\n", | |
" parse_url = Unicode('').tag(sync=True)\n" | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": 2, | |
"metadata": { | |
"collapsed": false | |
}, | |
"outputs": [ | |
{ | |
"data": { | |
"application/javascript": [ | |
"require.config({\n", | |
" paths: {\n", | |
" biojs: \"https://cdn.biojs.net/msa/0.4/msa.min.gz.js\",\n", | |
" }\n", | |
"});\n", | |
"\n", | |
"require(['biojs'], function(fasta){\n", | |
" console.log(\"biojs loaded\");\n", | |
"});\n", | |
"\n", | |
"require([\"nbextensions/widgets/widgets/js/widget\",\n", | |
" \"nbextensions/widgets/widgets/js/manager\",\n", | |
" \"biojs\"],\n", | |
" function(widgets, manager, biojs){\n", | |
"});\n", | |
"\n", | |
"define('MsaParseURL', ['jquery', 'jupyter-js-widgets'], function($, widgets) {\n", | |
" var MsaParseUrlView = widgets.DOMWidgetView.extend({\n", | |
" render: function(){\n", | |
" var clustal = require(\"biojs-io-clustal\");\n", | |
" var m = new msa({\n", | |
" el:this.$el.append(\"<div>\", {id:\"seqDiv\"}),\n", | |
" });\n", | |
" clustal.read(this.model.get(\"parse_url\"), function(err, seqs){\n", | |
" m.seqs.reset(seqs);\n", | |
" m.render();\n", | |
" });\n", | |
" },\n", | |
" });\n", | |
" manager.WidgetManager.register_widget_view('MsaParseUrlView', MsaParseUrlView);\n", | |
" return {\n", | |
" MsaParseUrlView: MsaParseUrlView\n", | |
" }\n", | |
"});" | |
], | |
"text/plain": [ | |
"<IPython.core.display.Javascript object>" | |
] | |
}, | |
"metadata": {}, | |
"output_type": "display_data" | |
} | |
], | |
"source": [ | |
"%%javascript\n", | |
"require.config({\n", | |
" paths: {\n", | |
" biojs: \"https://cdn.biojs.net/msa/0.4/msa.min.gz.js\",\n", | |
" }\n", | |
"});\n", | |
"\n", | |
"require(['biojs'], function(fasta){\n", | |
" console.log(\"biojs loaded\");\n", | |
"});\n", | |
"\n", | |
"require([\"nbextensions/widgets/widgets/js/widget\",\n", | |
" \"nbextensions/widgets/widgets/js/manager\",\n", | |
" \"biojs\"],\n", | |
" function(widgets, manager, biojs){\n", | |
"});\n", | |
"\n", | |
"define('MsaParseURL', ['jquery', 'jupyter-js-widgets'], function($, widgets) {\n", | |
" var MsaParseUrlView = widgets.DOMWidgetView.extend({\n", | |
" render: function(){\n", | |
" var clustal = require(\"biojs-io-clustal\");\n", | |
" var m = new msa({\n", | |
" el:this.$el.append(\"<div>\", {id:\"seqDiv\"}),\n", | |
" });\n", | |
" clustal.read(this.model.get(\"parse_url\"), function(err, seqs){\n", | |
" m.seqs.reset(seqs);\n", | |
" m.render();\n", | |
" });\n", | |
" },\n", | |
" });\n", | |
" manager.WidgetManager.register_widget_view('MsaParseUrlView', MsaParseUrlView);\n", | |
" return {\n", | |
" MsaParseUrlView: MsaParseUrlView\n", | |
" }\n", | |
"});\n" | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": 3, | |
"metadata": { | |
"collapsed": false | |
}, | |
"outputs": [], | |
"source": [ | |
"w = MsaParseUrl()\n" | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": 4, | |
"metadata": { | |
"collapsed": false | |
}, | |
"outputs": [], | |
"source": [ | |
"w.parse_url = \"https://raw.githubusercontent.com/greenify/msa/master/test/dummy/samples/p53.clustalo.clustal\"" | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": 5, | |
"metadata": { | |
"collapsed": true | |
}, | |
"outputs": [], | |
"source": [ | |
"display(w)" | |
] | |
}, | |
{ | |
"cell_type": "code", | |
"execution_count": null, | |
"metadata": { | |
"collapsed": true | |
}, | |
"outputs": [], | |
"source": [] | |
} | |
], | |
"metadata": { | |
"kernelspec": { | |
"display_name": "Python 2", | |
"language": "python", | |
"name": "python2" | |
}, | |
"language_info": { | |
"codemirror_mode": { | |
"name": "ipython", | |
"version": 2 | |
}, | |
"file_extension": ".py", | |
"mimetype": "text/x-python", | |
"name": "python", | |
"nbconvert_exporter": "python", | |
"pygments_lexer": "ipython2", | |
"version": "2.7.11" | |
}, | |
"widgets": { | |
"state": {}, | |
"version": "1.1.0" | |
} | |
}, | |
"nbformat": 4, | |
"nbformat_minor": 0 | |
} |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment