several fixes for consistency and for python 2 compatibility

ibmstafa · Jul 14, 2015 · 0f810c8 · 0f810c8
1 parent 14bbb54
commit 0f810c8
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Showing 17 changed files with 299 additions and 780 deletions.
diff --git a/1.01_StringBasics.ipynb b/1.01_StringBasics.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 1,
    "metadata": {
     "collapsed": false
    },
@@ -14,7 +14,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 2,
    "metadata": {
     "collapsed": true
    },
@@ -26,7 +26,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 3,
    "metadata": {
     "collapsed": false
    },
@@ -37,7 +37,7 @@
        "'C'"
       ]
      },
-     "execution_count": 4,
+     "execution_count": 3,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -49,7 +49,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 4,
    "metadata": {
     "collapsed": false
    },
@@ -60,7 +60,7 @@
        "4"
       ]
      },
-     "execution_count": 5,
+     "execution_count": 4,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -72,7 +72,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 5,
    "metadata": {
     "collapsed": false
    },
@@ -84,7 +84,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 6,
    "metadata": {
     "collapsed": false
    },
@@ -95,7 +95,7 @@
        "0"
       ]
      },
-     "execution_count": 7,
+     "execution_count": 6,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -106,7 +106,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 7,
    "metadata": {
     "collapsed": false
    },
@@ -128,7 +128,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 8,
    "metadata": {
     "collapsed": false
    },
@@ -148,7 +148,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 9,
    "metadata": {
     "collapsed": false
    },
@@ -159,7 +159,7 @@
        "'T'"
       ]
      },
-     "execution_count": 10,
+     "execution_count": 9,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -172,7 +172,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
+   "execution_count": 10,
    "metadata": {
     "collapsed": false
    },
@@ -181,7 +181,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "CAAGTTATGC\n"
+      "TCAATTCCAT\n"
      ]
     }
    ],
@@ -195,7 +195,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 15,
+   "execution_count": 11,
    "metadata": {
     "collapsed": false
    },
@@ -204,7 +204,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "GGCTCATTGA\n"
+      "GATCACCGAC\n"
      ]
     }
    ],
@@ -216,18 +216,18 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 16,
+   "execution_count": 12,
    "metadata": {
     "collapsed": false
    },
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "'GC'"
+       "'AT'"
       ]
      },
-     "execution_count": 16,
+     "execution_count": 12,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -239,18 +239,18 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 17,
+   "execution_count": 13,
    "metadata": {
     "collapsed": false
    },
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "'GGC'"
+       "'GAT'"
       ]
      },
-     "execution_count": 17,
+     "execution_count": 13,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -262,18 +262,18 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 18,
+   "execution_count": 14,
    "metadata": {
     "collapsed": false
    },
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "'TGA'"
+       "'GAC'"
       ]
      },
-     "execution_count": 18,
+     "execution_count": 14,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -285,18 +285,18 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 19,
+   "execution_count": 15,
    "metadata": {
     "collapsed": false
    },
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "'TGA'"
+       "'GAC'"
       ]
      },
-     "execution_count": 19,
+     "execution_count": 15,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -323,7 +323,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.4.2"
+   "version": "3.4.3"
   }
  },
  "nbformat": 4,

diff --git a/1.02_ManipulatingDNAStrings.ipynb b/1.02_ManipulatingDNAStrings.ipynb
@@ -178,7 +178,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.4.2"
+   "version": "3.4.3"
   }
  },
  "nbformat": 4,

diff --git a/1.03_ParsingRefGenome.ipynb b/1.03_ParsingRefGenome.ipynb
@@ -11,23 +11,23 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "--2015-03-24 11:41:37--  https://d28rh4a8wq0iu5.cloudfront.net/ads1/data/lambda_virus.fa\n",
-      "Resolving d28rh4a8wq0iu5.cloudfront.net... 54.192.100.45, 54.230.103.66, 216.137.33.105, ...\n",
-      "Connecting to d28rh4a8wq0iu5.cloudfront.net|54.192.100.45|:443... connected.\n",
+      "--2015-07-14 11:22:01--  http://d28rh4a8wq0iu5.cloudfront.net/ads1/data/lambda_virus.fa\n",
+      "Resolving d28rh4a8wq0iu5.cloudfront.net... 54.192.54.85, 54.192.54.222, 54.192.55.189, ...\n",
+      "Connecting to d28rh4a8wq0iu5.cloudfront.net|54.192.54.85|:80... connected.\n",
       "HTTP request sent, awaiting response... 200 OK\n",
       "Length: 49270 (48K) [application/octet-stream]\n",
       "Saving to: 'lambda_virus.fa'\n",
       "\n",
-      "100%[======================================>] 49,270      --.-K/s   in 0.02s   \n",
+      "lambda_virus.fa     100%[=====================>]  48.12K  --.-KB/s   in 0.1s   \n",
       "\n",
-      "2015-03-24 11:41:38 (2.39 MB/s) - 'lambda_virus.fa' saved [49270/49270]\n",
+      "2015-07-14 11:22:01 (386 KB/s) - 'lambda_virus.fa' saved [49270/49270]\n",
       "\n"
      ]
     }
    ],
    "source": [
     "# Following line downloads FASTA file containing the lambda phage reference genome\n",
-    "!wget --no-check https://d28rh4a8wq0iu5.cloudfront.net/ads1/data/lambda_virus.fa"
+    "!wget http://d28rh4a8wq0iu5.cloudfront.net/ads1/data/lambda_virus.fa"
    ]
   },
   {
@@ -72,7 +72,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "{'T': 11986, 'C': 11362, 'A': 12334, 'G': 12820}\n"
+      "{'G': 12820, 'T': 11986, 'A': 12334, 'C': 11362}\n"
      ]
     }
    ],
@@ -106,15 +106,6 @@
     "import collections\n",
     "collections.Counter(genome)"
    ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {
-    "collapsed": true
-   },
-   "outputs": [],
-   "source": []
   }
  ],
  "metadata": {
@@ -133,7 +124,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.4.2"
+   "version": "3.4.3"
   }
  },
  "nbformat": 4,