--- a
+++ b/exseek/templates/fastqc.ipynb
@@ -0,0 +1,69 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import pandas as pd\n",
+    "import numpy as np"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "summary = pd.read_table('fastqc.txt', sep='\\t')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "summary.set_index('sample_id', inplace=True, drop=False)\n",
+    "qc_status = summary.iloc[:, 9:].copy()\n",
+    "qc_status.fillna('NA')\n",
+    "qc_status = qc_status.astype('str')\n",
+    "sample_ids = qc_status.index.values\n",
+    "sections = qc_status.columns.values\n",
+    "def style_func(val):\n",
+    "    status, row, col = val.split('|')\n",
+    "    row, col = int(row), int(col)\n",
+    "    color = {'pass': 'green', 'fail': 'red', 'warn': 'orange'}.get(status, 'gray')\n",
+    "    return '<a href=\"../fastqc/{sample_id}_fastqc.html#M{section}\" style=\"color: {color}\">{status}</a>'.format(\n",
+    "        sample_id=sample_ids[row], color=color, status=status, section=col)\n",
+    "\n",
+    "pd.DataFrame(qc_status.values \\\n",
+    "             + '|' + np.arange(qc_status.shape[0]).astype('str')[:, np.newaxis] \\\n",
+    "             + '|' + np.arange(qc_status.shape[1]).astype('str')[np.newaxis, :],\n",
+    "             index=qc_status.index, columns=qc_status.columns) \\\n",
+    "    .style.format(style_func)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernel_spec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "laugnage_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "version": "3.6"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}