Merge pull request #28 from bcgsc/main

Update from main branch

Figures/Methylation/Methylation_Fig4a.ipynb

@@ -2,20 +2,20 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
-    "# title: Codes to generate methylation plots\n",
-    "# author: Andrew Galbraith\n",
-    "# Modules to import\n",
+    "# Modules to import - get rid of any not used - add to dockfile in github\n",
     "import pandas as pd\n",
     "import scipy\n",
     "import datashader as ds\n",
     "from datashader.mpl_ext import dsshow\n",
     "import scipy.stats\n",
     "import matplotlib.pyplot as plt\n",
-    "from matplotlib.colors import LinearSegmentedColormap\n"
+    "from matplotlib.colors import LinearSegmentedColormap\n",
+    "import ssl\n",
+    "from urllib.request import urlopen\n"
    ]
   },
   {
@@ -24,8 +24,16 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# import data\n",
-    "POG044_BS_Nano_df = pd.read_csv('https://www.bcgsc.ca/downloads/nanopore_pog/Methylation/POG044_BS_Nanopolish_Meth.bed.gz', sep=\"\\t\",header=None, compression='gzip')\n"
+    "# import data - make sure to change to data from GSC website\n",
+    "\n",
+    "# use ssl to securely open csv before loading into pandas dataframe\n",
+    "data_loc = 'https://www.bcgsc.ca/downloads/nanopore_pog/Methylation/POG044_BS_Nanopolish_Meth.bed.gz'\n",
+    "\n",
+    "context=ssl.create_default_context()\n",
+    "context.set_ciphers(\"DEFAULT\")\n",
+    "result = urlopen(data_loc, context=context)\n",
+    "\n",
+    "POG044_BS_Nano_df = pd.read_csv(result, sep=\"\\t\",header=None, compression='gzip')\n"
    ]
   },
   {