{ "cells": [ { "cell_type": "code", "execution_count": 1, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Populating the interactive namespace from numpy and matplotlib\n" ] } ], "source": [ "%pylab inline\n", "import gepyto\n", "from gepyto.structures.genes import Gene\n", "\n", "import matplotlib.pyplot as plt" ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n" ] } ], "source": [ "# Load a gene from Ensembl\n", "g = Gene.factory_symbol(\"CKM\")\n", "\n", "# This gene has only one transcript so we will\n", "# get the corresponding sequence.\n", "s = g.transcripts[0].get_sequence(\"protein\")\n", "print s" ] }, { "cell_type": "code", "execution_count": 3, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "pan_troglodytes \n" ] }, { "data": { "text/plain": [ "" ] }, 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compute the base-base correlation and plot it.\n", "bbc = s.bbc(k=50)\n", "\n", "# We can also compare this to an ortholog.\n", "orthos = g.get_ortholog_sequences()\n", "ortho = orthos[0]\n", "print ortho.info[\"species\"], ortho\n", "ortho_bbc = ortho.bbc(k=50)\n", "\n", "# And to anothe human gene.\n", "g2 = Gene.factory_symbol(\"LILRB5\")\n", "other_bbc = g2.transcripts[0].get_sequence(\"protein\").bbc(k=50)\n", "\n", "fig, axes = plt.subplots(1, 3, figsize=(15, 4))\n", "axes[0].imshow(bbc.reshape(20, 20), interpolation='none')\n", "axes[0].set_xlabel(\"Human CKM\")\n", "\n", "axes[1].imshow(ortho_bbc.reshape(20, 20), interpolation='none')\n", "axes[1].set_xlabel(\"Gorilla CKM\")\n", "\n", "axes[2].imshow(other_bbc.reshape(20, 20), interpolation='none')\n", "axes[2].set_xlabel(\"Human LILRB5\")" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "As you can see, the BBC profiles for the orthologs are more similar than for another human gene I picked off the top of my head. This was just a short showcase of ``gepyto`` capabilities with respect to sequence analysis and easy homology or sequence queries." ] } ], "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": "2.7.8" } }, "nbformat": 4, "nbformat_minor": 0 }