{ "cells": [ { "cell_type": "code", "execution_count": 21, "metadata": {}, "outputs": [], "source": [ "# For motifs analysis and manipulations\n", "from Bio import motifs\n", "\n", "# For reading input files\n", "import h5py\n", "\n", "# Math and data manipulation tools \n", "import pandas as pd\n", "import numpy as np\n", "\n", "# plotting\n", "import matplotlib as mpl\n", "import matplotlib.pyplot as plt\n", "import seaborn as sns\n", "sns.set_style('whitegrid')\n", "%matplotlib inline" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "['../DATA/motifs_out/model_out.h5', '../DATA/motifs_out/sample.h5']" ] }, "execution_count": 3, "metadata": {}, "output_type": "execute_result" } ], "source": [ "import glob\n", "glob.glob(\"../DATA/motifs_out/*.h5\")" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [], "source": [ "dataset = h5py.File(\"../DATA/motifs_out/model_out.h5\", 'r')" ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "['outs', 'weights']" ] }, "execution_count": 5, "metadata": {}, "output_type": "execute_result" } ], "source": [ "list(dataset.keys())" ] }, { "cell_type": "code", "execution_count": 7, "metadata": {}, "outputs": [], "source": [ "outs = dataset['outs'].value\n", "weights = dataset['weights'].value" ] }, { "cell_type": "code", "execution_count": 8, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "(1000, 300, 582)" ] }, "execution_count": 8, "metadata": {}, "output_type": "execute_result" } ], "source": [ "outs.shape" ] }, { "cell_type": "code", "execution_count": 9, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "(300, 4, 19)" ] }, "execution_count": 9, "metadata": {}, "output_type": "execute_result" } ], "source": [ "weights.shape" ] }, { "cell_type": "code", "execution_count": 87, "metadata": {}, "outputs": [], "source": [ "w = weights[0]\n", "norm = (w-np.min(w))/np.sum(w-np.min(w)" ] }, { "cell_type": "code", "execution_count": 88, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "(4, 19)" ] }, "execution_count": 88, "metadata": {}, "output_type": "execute_result" } ], "source": [ "w.shape" ] }, { "cell_type": "code", "execution_count": 89, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "" ] }, "execution_count": 89, "metadata": {}, "output_type": "execute_result" }, { "data": { "image/png": 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\n", 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" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "plt.figure(figsize=[10,3])\n", "sns.heatmap(norm, axis=0), cmap='RdBu_r')" ] }, { "cell_type": "code", "execution_count": 90, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "array([[0.2808151 , 0.38213084, 0.13436159, 0.35968034, 0.32117454,\n", " 0.22322443, 0.30827511, 0.31640019, 0.40647462, 0.40435883,\n", " 0.00865058, 0.1490017 , 0.21456887, 0.14177918, 0.19738375,\n", " 0.22377249, 0.29291809, 0.23277512, 0.27462113],\n", " [0.4000677 , 0.18380452, 0.26356109, 0.08737579, 0.02886923,\n", " 0.20950783, 0.12733266, 0.20573423, 0.05106849, 0.10626638,\n", " 0.47252076, 0.41882845, 0.39083344, 0.26310484, 0.23620693,\n", " 0.3562528 , 0.32169934, 0.1901722 , 0.33113507],\n", " [0.0934622 , 0. , 0.43152194, 0.21108214, 0.40561515,\n", " 0.22646 , 0.4112217 , 0.30054707, 0.28144087, 0.44267591,\n", " 0.48137252, 0.18045133, 0.19502669, 0.29398722, 0.24974067,\n", " 0.15544437, 0.07572803, 0.28798318, 0.18358438],\n", " [0.22565499, 0.43406464, 0.17055538, 0.34186173, 0.24434107,\n", " 0.34080774, 0.15317054, 0.17731851, 0.26101602, 0.04669888,\n", " 0.03745613, 0.25171852, 0.199571 , 0.30112875, 0.31666866,\n", " 0.26453034, 0.30965454, 0.28906949, 0.21065942]])" ] }, "execution_count": 90, "metadata": {}, "output_type": "execute_result" } ], "source": [ "for_saving = (w-np.min(w))/np.sum(w-np.min(w), axis=0)\n", "for_saving" ] }, { "cell_type": "code", "execution_count": 91, "metadata": {}, "outputs": [], "source": [ "np.savetxt(X=for_saving, fname='tmp.pfm', delimiter='\\t', fmt='%.2f')" ] }, { "cell_type": "code", "execution_count": 93, "metadata": {}, "outputs": [], "source": [ "motif = motifs.read(open('tmp.pfm','r' ), format='pfm')" ] }, { "cell_type": "code", "execution_count": 94, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "{'G': (0.09,\n", " 0.0,\n", " 0.4343434343434343,\n", " 0.21000000000000002,\n", " 0.41,\n", " 0.23,\n", " 0.41,\n", " 0.297029702970297,\n", " 0.28,\n", " 0.4399999999999999,\n", " 0.48,\n", " 0.18,\n", " 0.2,\n", " 0.29292929292929293,\n", " 0.24752475247524752,\n", " 0.16,\n", " 0.08,\n", " 0.29,\n", " 0.18181818181818182),\n", " 'A': (0.28,\n", " 0.38383838383838387,\n", " 0.1313131313131313,\n", " 0.36000000000000004,\n", " 0.32,\n", " 0.22,\n", " 0.31,\n", " 0.31683168316831684,\n", " 0.41,\n", " 0.3999999999999999,\n", " 0.01,\n", " 0.15,\n", " 0.21,\n", " 0.14141414141414144,\n", " 0.19801980198019803,\n", " 0.22,\n", " 0.29,\n", " 0.23,\n", " 0.27272727272727276),\n", " 'T': (0.23,\n", " 0.43434343434343436,\n", " 0.1717171717171717,\n", " 0.3400000000000001,\n", " 0.24,\n", " 0.34,\n", " 0.15,\n", " 0.1782178217821782,\n", " 0.26,\n", " 0.04999999999999999,\n", " 0.04,\n", " 0.25,\n", " 0.2,\n", " 0.30303030303030304,\n", " 0.31683168316831684,\n", " 0.26,\n", " 0.31,\n", " 0.29,\n", " 0.21212121212121213),\n", " 'C': (0.4,\n", " 0.18181818181818182,\n", " 0.2626262626262626,\n", " 0.09000000000000001,\n", " 0.03,\n", " 0.21,\n", " 0.13,\n", " 0.2079207920792079,\n", " 0.05,\n", " 0.10999999999999997,\n", " 0.47,\n", " 0.42,\n", " 0.39,\n", " 0.26262626262626265,\n", " 0.2376237623762376,\n", " 0.36,\n", " 0.32,\n", " 0.19,\n", " 0.33333333333333337)}" ] }, "execution_count": 94, "metadata": {}, "output_type": "execute_result" } ], "source": [ "#motif.consensus\n", "#len(motif.consensus)\n", "motif.pwm\n", "#motif.pssm " ] }, { "cell_type": "code", "execution_count": 95, "metadata": {}, "outputs": [], "source": [ "fname = \"tmp.png\"\n", "motif.weblogo(fname, format='PNG')" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [] } ], "metadata": { "kernelspec": { "display_name": "Python (distiller-editable)", "language": "python", "name": "distiller-editable" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.6.5" } }, "nbformat": 4, "nbformat_minor": 2 }