Demo of displaying GenomeDiagram objects in Jupyter

JupyterGenomeDiagram.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "from Bio.Graphics import GenomeDiagram\n",
    "from Bio.SeqFeature import SeqFeature, FeatureLocation\n",
    "from IPython.display import display, Image"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "<Bio.Graphics.GenomeDiagram._Feature.Feature at 0x1041cda20>"
      ]
     },
     "execution_count": 22,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "gd_diagram = GenomeDiagram.Diagram(\"Test diagram\")\n",
    "gd_track_for_features = gd_diagram.new_track(1, name=\"Annotated Features\")\n",
    "gd_feature_set = gd_track_for_features.new_set()\n",
    "gd_feature_set.add_feature(SeqFeature(FeatureLocation(25, 75), strand=+1))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": "iVBORw0KGgoAAAANSUhEUgAAA0oAAAJTCAIAAAC5FnFdAAAL5ElEQVR4nO3aMUpcYRiG0Zlo0sQV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\npPwCsTNmXEKInhQAAAAASUVORK5CYII=\n",
      "text/plain": [
       "<IPython.core.display.Image object>"
      ]
     },
     "execution_count": 23,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "gd_diagram.draw(format=\"linear\", orientation=\"landscape\", pagesize='A4',\n",
    "                fragments=1, start=0, end=100)\n",
    "Image(gd_diagram.write_to_string(\"PNG\"))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
 ],
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  "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": "3.6.1"
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 },
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