{ "cells": [ { "cell_type": "code", "execution_count": 5, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/html": [ "\n", "
\n", " \n", " Loading BokehJS ...\n", "
" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/javascript": [ "\n", "(function(global) {\n", " function now() {\n", " return new Date();\n", " }\n", "\n", " var force = true;\n", "\n", " if (typeof (window._bokeh_onload_callbacks) === \"undefined\" || force === true) {\n", " window._bokeh_onload_callbacks = [];\n", " window._bokeh_is_loading = undefined;\n", " }\n", "\n", "\n", " \n", " if (typeof (window._bokeh_timeout) === \"undefined\" || force === true) {\n", " window._bokeh_timeout = Date.now() + 5000;\n", " window._bokeh_failed_load = false;\n", " }\n", "\n", " var NB_LOAD_WARNING = {'data': {'text/html':\n", " \"
\\n\"+\n", " \"

\\n\"+\n", " \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n", " \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n", " \"

\\n\"+\n", " \"\\n\"+\n", " \"\\n\"+\n", " \"from bokeh.resources import INLINE\\n\"+\n", " \"output_notebook(resources=INLINE)\\n\"+\n", " \"\\n\"+\n", " \"
\"}};\n", "\n", " function display_loaded() {\n", " if (window.Bokeh !== undefined) {\n", " var el = document.getElementById(\"a8ee067f-8f6a-43e6-93f2-75a5d306ba73\");\n", " el.textContent = \"BokehJS \" + Bokeh.version + \" successfully loaded.\";\n", " } else if (Date.now() < window._bokeh_timeout) {\n", " setTimeout(display_loaded, 100)\n", " }\n", " }\n", "\n", " function run_callbacks() {\n", " try {\n", " window._bokeh_onload_callbacks.forEach(function(callback) { callback() });\n", " }\n", " finally {\n", " delete window._bokeh_onload_callbacks\n", " }\n", " console.info(\"Bokeh: all callbacks have finished\");\n", " }\n", "\n", " function load_libs(js_urls, callback) {\n", " window._bokeh_onload_callbacks.push(callback);\n", " if (window._bokeh_is_loading > 0) {\n", " console.log(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n", " return null;\n", " }\n", " if (js_urls == null || js_urls.length === 0) {\n", " run_callbacks();\n", " return null;\n", " }\n", " console.log(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n", " window._bokeh_is_loading = js_urls.length;\n", " for (var i = 0; i < js_urls.length; i++) {\n", " var url = js_urls[i];\n", " var s = document.createElement('script');\n", " s.src = url;\n", " s.async = false;\n", " s.onreadystatechange = s.onload = function() {\n", " window._bokeh_is_loading--;\n", " if (window._bokeh_is_loading === 0) {\n", " console.log(\"Bokeh: all BokehJS libraries loaded\");\n", " run_callbacks()\n", " }\n", " };\n", " s.onerror = function() {\n", " console.warn(\"failed to load library \" + url);\n", " };\n", " console.log(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", " document.getElementsByTagName(\"head\")[0].appendChild(s);\n", " }\n", " };var element = document.getElementById(\"a8ee067f-8f6a-43e6-93f2-75a5d306ba73\");\n", " if (element == null) {\n", " console.log(\"Bokeh: ERROR: autoload.js configured with elementid 'a8ee067f-8f6a-43e6-93f2-75a5d306ba73' but no matching script tag was found. \")\n", " return false;\n", " }\n", "\n", " var js_urls = [\"https://cdn.pydata.org/bokeh/release/bokeh-0.12.6.min.js\", \"https://cdn.pydata.org/bokeh/release/bokeh-widgets-0.12.6.min.js\"];\n", "\n", " var inline_js = [\n", " function(Bokeh) {\n", " Bokeh.set_log_level(\"info\");\n", " },\n", " \n", " function(Bokeh) {\n", " \n", " },\n", " \n", " function(Bokeh) {\n", " \n", " document.getElementById(\"a8ee067f-8f6a-43e6-93f2-75a5d306ba73\").textContent = \"BokehJS is loading...\";\n", " },\n", " function(Bokeh) {\n", " console.log(\"Bokeh: injecting CSS: https://cdn.pydata.org/bokeh/release/bokeh-0.12.6.min.css\");\n", " Bokeh.embed.inject_css(\"https://cdn.pydata.org/bokeh/release/bokeh-0.12.6.min.css\");\n", " console.log(\"Bokeh: injecting CSS: https://cdn.pydata.org/bokeh/release/bokeh-widgets-0.12.6.min.css\");\n", " Bokeh.embed.inject_css(\"https://cdn.pydata.org/bokeh/release/bokeh-widgets-0.12.6.min.css\");\n", " }\n", " ];\n", "\n", " function run_inline_js() {\n", " \n", " if ((window.Bokeh !== undefined) || (force === true)) {\n", " for (var i = 0; i < inline_js.length; i++) {\n", " inline_js[i](window.Bokeh);\n", " }if (force === true) {\n", " display_loaded();\n", " }} else if (Date.now() < window._bokeh_timeout) {\n", " setTimeout(run_inline_js, 100);\n", " } else if (!window._bokeh_failed_load) {\n", " console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n", " window._bokeh_failed_load = true;\n", " } else if (force !== true) {\n", " var cell = $(document.getElementById(\"a8ee067f-8f6a-43e6-93f2-75a5d306ba73\")).parents('.cell').data().cell;\n", " cell.output_area.append_execute_result(NB_LOAD_WARNING)\n", " }\n", "\n", " }\n", "\n", " if (window._bokeh_is_loading === 0) {\n", " console.log(\"Bokeh: BokehJS loaded, going straight to plotting\");\n", " run_inline_js();\n", " } else {\n", " load_libs(js_urls, function() {\n", " console.log(\"Bokeh: BokehJS plotting callback run at\", now());\n", " run_inline_js();\n", " });\n", " }\n", "}(this));" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "from Bio import SeqIO\n", "from bokeh.io import output_notebook, push_notebook\n", "from bokeh.plotting import figure, show\n", "from bokeh.models.tools import BoxZoomTool\n", "from bokeh.models.tickers import FixedTicker\n", "from bokeh.models import Range1d,LinearAxis\n", "import numpy as np\n", "output_notebook()" ] }, { "cell_type": "code", "execution_count": 10, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/html": [ "\n", "\n", "
\n", "
\n", "
\n", "" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "seq = SeqIO.read('/home/tboland/SAD7743_P01_E09_LC_E09.ab1', 'abi')\n", "quality = seq.letter_annotations['phred_quality']\n", "peak_calls = seq.annotations['abif_raw']['PLOC2']\n", "order = seq.annotations['abif_raw']['FWO_1']\n", "sequence = str(seq.seq)\n", "\n", "# Extract color data\n", "peaks = {}\n", "for i, (base, r) in enumerate(zip(order, [9, 10, 11, 12])):\n", " peaks[base] = seq.annotations['abif_raw']['DATA{}'.format(r)]\n", "\n", "# Plot\n", "p = figure(\n", " plot_width=900,\n", " plot_height=400,\n", " output_backend=\"webgl\",\n", " tools=['xpan', 'reset','xwheel_zoom', BoxZoomTool(dimensions='width')],\n", " active_drag='xpan',\n", " active_scroll='xwheel_zoom',\n", " title=seq.id\n", ")\n", "\n", "# Plot quality\n", "p.extra_y_ranges = {\"q\": Range1d(start=0, end=100)}\n", "p.add_layout(LinearAxis(y_range_name=\"q\"), 'right')\n", "p.rect(x=peak_calls, y=np.array(quality)/2, width=14, height=quality, y_range_name='q', color='#e7ecf6')\n", "\n", "# Plot colors\n", "for color, base in zip(['red', 'green', 'blue', 'black'], ['T', 'A', 'C', 'G']):\n", " peak = peaks[base]\n", " p.line(range(len(peak)), peak, line_color=color, legend=base)\n", "\n", "# Adjust tickers/ranges\n", "p.xaxis.ticker = FixedTicker(ticks=peak_calls)\n", "p.xaxis.major_label_overrides = dict(zip(peak_calls, sequence))\n", "p.y_range = Range1d(0, max(max(x) for x in peaks.values()))\n", "\n", "show(p)" ] } ], "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": "2.7.9" } }, "nbformat": 4, "nbformat_minor": 0 }