Minor update on descriptions and last part

Replaced some terminology with clearer language. For the last part, rearranged the cells so that the descriptive text matches with the corresponding script to be saved. Minor code update for the scripts at the end, from the format "not x in y" to "x not in y".

Author: zmielko

intro-programming-python-instructor.ipynb

@@ -30,7 +30,7 @@
     }
    },
    "source": [
-    "## Python & Notebook"
+    "## Python in the Jupyter Notebook Environment"
    ]
   },
   {
@@ -46,7 +46,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The gray boxes are cells. We write code in the cells with instructions for the computer to execute. Let's start by telling the computer to add 5 and 3 and print the result. "
+    "The gray boxes are cells. We write code in the cells with instructions for the computer to execute. Let's start by adding 5 and 3 and printing the result. "
    ]
   },
   {
@@ -87,10 +87,10 @@
    "outputs": [
     {
      "ename": "SyntaxError",
-     "evalue": "invalid syntax (<ipython-input-2-50b4ae29d403>, line 1)",
+     "evalue": "invalid syntax (3449611317.py, line 1)",
      "output_type": "error",
      "traceback": [
-      "\u001b[0;36m  File \u001b[0;32m\"<ipython-input-2-50b4ae29d403>\"\u001b[0;36m, line \u001b[0;32m1\u001b[0m\n\u001b[0;31m    print(Hello world)\u001b[0m\n\u001b[0m                    ^\u001b[0m\n\u001b[0;31mSyntaxError\u001b[0m\u001b[0;31m:\u001b[0m invalid syntax\n"
+      "\u001b[0;36m  Input \u001b[0;32mIn [2]\u001b[0;36m\u001b[0m\n\u001b[0;31m    print(Hello world)\u001b[0m\n\u001b[0m                ^\u001b[0m\n\u001b[0;31mSyntaxError\u001b[0m\u001b[0;31m:\u001b[0m invalid syntax\n"
      ]
     }
    ],
@@ -102,7 +102,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "OK so Python didn't like that, but there's a lot to learn here\n",
+    "OK so Python returned an error, but there's a lot to learn here:\n",
     "\n",
     "- Errors can be really helpful.\n",
     "- It's common to make mistakes, don't be discouraged\n",
@@ -205,7 +205,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "And we can print multiple things by inserting commas. So let's all greet our neighbor:"
+    "And we can print multiple items by inserting commas. So we can combine our greeting and neighbor to greet our neighbor:"
    ]
   },
   {
@@ -340,7 +340,7 @@
      "traceback": [
       "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
       "\u001b[0;31mTypeError\u001b[0m                                 Traceback (most recent call last)",
-      "\u001b[0;32m<ipython-input-11-6fb37bd547ba>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m      1\u001b[0m \u001b[0mmy_float\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;36m50.0\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      2\u001b[0m \u001b[0mmy_string\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m\"Hello\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 3\u001b[0;31m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmy_float\u001b[0m \u001b[0;34m+\u001b[0m \u001b[0mmy_string\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
+      "Input \u001b[0;32mIn [11]\u001b[0m, in \u001b[0;36m<cell line: 3>\u001b[0;34m()\u001b[0m\n\u001b[1;32m      1\u001b[0m my_float \u001b[38;5;241m=\u001b[39m \u001b[38;5;241m50.0\u001b[39m\n\u001b[1;32m      2\u001b[0m my_string \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mHello\u001b[39m\u001b[38;5;124m\"\u001b[39m\n\u001b[0;32m----> 3\u001b[0m \u001b[38;5;28mprint\u001b[39m(\u001b[43mmy_float\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m+\u001b[39;49m\u001b[43m \u001b[49m\u001b[43mmy_string\u001b[49m)\n",
       "\u001b[0;31mTypeError\u001b[0m: unsupported operand type(s) for +: 'float' and 'str'"
      ]
     }
@@ -508,7 +508,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "One more optional parameter you can use is called a step in the format **[start:end:step]**. This parameter determines what you \"count by\" and is 1 by default. "
+    "One more optional parameter you can use is called a **step** in the format **[start:end:step]**. This parameter determines what you \"count by\" and is 1 by default. "
    ]
   },
   {
@@ -793,10 +793,10 @@
    "outputs": [
     {
      "ename": "SyntaxError",
-     "evalue": "invalid syntax (<ipython-input-28-3051ded84a5c>, line 1)",
+     "evalue": "invalid syntax (3233142308.py, line 1)",
      "output_type": "error",
      "traceback": [
-      "\u001b[0;36m  File \u001b[0;32m\"<ipython-input-28-3051ded84a5c>\"\u001b[0;36m, line \u001b[0;32m1\u001b[0m\n\u001b[0;31m    1a\u001b[0m\n\u001b[0m     ^\u001b[0m\n\u001b[0;31mSyntaxError\u001b[0m\u001b[0;31m:\u001b[0m invalid syntax\n"
+      "\u001b[0;36m  Input \u001b[0;32mIn [28]\u001b[0;36m\u001b[0m\n\u001b[0;31m    1a\u001b[0m\n\u001b[0m     ^\u001b[0m\n\u001b[0;31mSyntaxError\u001b[0m\u001b[0;31m:\u001b[0m invalid syntax\n"
      ]
     }
    ],
@@ -866,7 +866,7 @@
      "traceback": [
       "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
       "\u001b[0;31mTypeError\u001b[0m                                 Traceback (most recent call last)",
-      "\u001b[0;32m<ipython-input-31-74803fcdf01e>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mr3\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m2\u001b[0m\u001b[0;34m]\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m'G'\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
+      "Input \u001b[0;32mIn [31]\u001b[0m, in \u001b[0;36m<cell line: 1>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0m r3[\u001b[38;5;241m2\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mG\u001b[39m\u001b[38;5;124m'\u001b[39m\n",
       "\u001b[0;31mTypeError\u001b[0m: 'str' object does not support item assignment"
      ]
     }
@@ -1110,7 +1110,7 @@
     }
    ],
    "source": [
-    "my_dictionary = {\"key\":\"value\", \"second_key\":2, 3:\"third_value\"}\n",
+    "my_dictionary = {\"key\": \"value\", \"second_key\": 2, 3: \"third_value\"}\n",
     "print(my_dictionary)"
    ]
   },
@@ -1281,7 +1281,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "As an exercise, let's get the total quantity of nucleotides we have. This loop should look a lot like counting the bases in the sequence"
+    "As an exercise, let's get the total quantity of nucleotides we have in the dictionary counts. This loop should look a lot like counting the bases in the sequence."
    ]
   },
   {
@@ -1404,7 +1404,7 @@
     "\n",
     "We've looked at strings and dictionaries as collection types. There's another one that's really useful, and it's called a list. It's an ordered collection of elements. Lists use the `[]` square brackets, and elments are separated by commas.\n",
     "\n",
-    "Here's one that contains our 3 sequences.:"
+    "Here's one that contains our 3 sequences."
    ]
   },
   {
@@ -1516,7 +1516,7 @@
    "source": [
     "### Making choices / Conditionals\n",
     "\n",
-    "When writing programs, it's very handy to examine some data or some results, and make a decision about what to do next. This is called a conditional, and most common version is the `if-else`.\n",
+    "When writing programs, it's usefull to examine some data or some results, and make a decision about what to do next. This is called a conditional, and most common version is the `if-else`.\n",
     "\n",
     "Here's how it works. we start with an `if` keyword, and then we write some expression that will either be **True** or **False**. Then we write a colon, and indent what should happen **if** the expression was **True**. \n",
     "\n",
@@ -2034,7 +2034,7 @@
       " |  index(...)\n",
       " |      S.index(sub[, start[, end]]) -> int\n",
       " |      \n",
-      " |      Return the lowest index in S where substring sub is found, \n",
+      " |      Return the lowest index in S where substring sub is found,\n",
       " |      such that sub is contained within S[start:end].  Optional\n",
       " |      arguments start and end are interpreted as in slice notation.\n",
       " |      \n",
@@ -2073,8 +2073,8 @@
       " |  isidentifier(self, /)\n",
       " |      Return True if the string is a valid Python identifier, False otherwise.\n",
       " |      \n",
-      " |      Use keyword.iskeyword() to test for reserved identifiers such as \"def\" and\n",
-      " |      \"class\".\n",
+      " |      Call keyword.iskeyword(s) to test whether string s is a reserved identifier,\n",
+      " |      such as \"def\" or \"class\".\n",
       " |  \n",
       " |  islower(self, /)\n",
       " |      Return True if the string is a lowercase string, False otherwise.\n",
@@ -2143,6 +2143,19 @@
       " |      If the separator is not found, returns a 3-tuple containing the original string\n",
       " |      and two empty strings.\n",
       " |  \n",
+      " |  removeprefix(self, prefix, /)\n",
+      " |      Return a str with the given prefix string removed if present.\n",
+      " |      \n",
+      " |      If the string starts with the prefix string, return string[len(prefix):].\n",
+      " |      Otherwise, return a copy of the original string.\n",
+      " |  \n",
+      " |  removesuffix(self, suffix, /)\n",
+      " |      Return a str with the given suffix string removed if present.\n",
+      " |      \n",
+      " |      If the string ends with the suffix string and that suffix is not empty,\n",
+      " |      return string[:-len(suffix)]. Otherwise, return a copy of the original\n",
+      " |      string.\n",
+      " |  \n",
       " |  replace(self, old, new, count=-1, /)\n",
       " |      Return a copy with all occurrences of substring old replaced by new.\n",
       " |      \n",
@@ -2268,7 +2281,7 @@
       " |  __new__(*args, **kwargs) from builtins.type\n",
       " |      Create and return a new object.  See help(type) for accurate signature.\n",
       " |  \n",
-      " |  maketrans(x, y=None, z=None, /)\n",
+      " |  maketrans(...)\n",
       " |      Return a translation table usable for str.translate().\n",
       " |      \n",
       " |      If there is only one argument, it must be a dictionary mapping Unicode\n",
@@ -2303,7 +2316,7 @@
     "3. Reverses their order\n",
     "4. (Bonus) Print the first letter from each word\n",
     "\n",
-    "Hint: Use the `help()` function on `str` and `list` to see what methods are available to assist with the task. "
+    "**Hint:** Use the `help()` function on `str` and `list` to see what methods are available to assist with the task. "
    ]
   },
   {
@@ -2536,7 +2549,9 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "To test that the function works, we could eyeball it, and we can also test that double-reversing gives us the original sequence:"
+    "To test that the function works, we could:\n",
+    "- see if the output is correct ourselves\n",
+    "- test that double-reversing gives us the original sequence"
    ]
   },
   {
@@ -3037,14 +3052,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "We've done a good job of organizing our code into functions here, but we've only been running them from this notebook. So next, we're going to take our code and put it in a script - starting with the `read_sequence` function.\n"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "This is going to be very familiar, since we're doing the same thing we did in bash, just with a different language!"
+    "We've done a good job of organizing our code into functions here, but we've only been running them from this notebook. So next, we're going to take our code and put it in a script - starting with the `read_fasta` function."
    ]
   },
   {
@@ -3081,7 +3089,7 @@
     "    f = open(filename)\n",
     "    for line in f:\n",
     "        line = line.strip()\n",
-    "        if not '>' in line:\n",
+    "        if '>' not in line:\n",
     "            # Append to the last sequence\n",
     "            sequence = sequence + line\n",
     "    f.close()\n",
@@ -3090,6 +3098,19 @@
     "print(read_fasta('ae.fa'))\n"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Our script reads our `ae.fa` file every time we run it, but we know most programs don't work that way. The programs we used in bash expected a data file as an *argument*, and that's a good convention for programs we write too.\n",
+    "\n",
+    "In Python, our program can get these arguments, but we have to load a module called `sys` from the standard library, a collection of modules included in python but not available by default. The documentation for these is part of the documentation for python: https://docs.python.org/3/library/sys.html\n",
+    "\n",
+    "Libraries are incredibly useful - there are libraries for working with numeric and scientific data, generating plots, fetching data from the web, working with image and document files, databases, etc. And of course, there's a library for getting things like your script's command-line arguments.\n",
+    "\n",
+    "So, let's change our `read_fasta.py` program slightly."
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -3105,7 +3126,7 @@
     "    f = open(filename)\n",
     "    for line in f:\n",
     "        line = line.strip()\n",
-    "        if not '>' in line:\n",
+    "        if '>' not in line:\n",
     "            # Append to the last sequence\n",
     "            sequence = sequence + line\n",
     "    f.close()\n",
@@ -3114,6 +3135,13 @@
     "print(read_fasta(sys.argv[1]))\n"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "But what happens if we don't have an input file name? According to the documentation, sys.argv, returns a list where the first item sys.argv[0] is the name of the script by default, and each additional item in the list are the command line arguments. If no argument was passed, sys.argv should be a list of just the script name."
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -3129,52 +3157,19 @@
     "    f = open(filename)\n",
     "    for line in f:\n",
     "        line = line.strip()\n",
-    "        if not '>' in line:\n",
+    "        if '>' not in line:\n",
     "            # Append to the last sequence\n",
     "            sequence = sequence + line\n",
     "    f.close()\n",
     "    return sequence\n",
     "\n",
     "if len(sys.argv) < 2:\n",
     "    print('Usage:', sys.argv[0], '<sequence.fa>')\n",
-    "    exit(1)\n",
+    "    sys.exit(1)\n",
     "\n",
     "print(read_fasta(sys.argv[1]))\n"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "`$ python read_fasta.py`"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Our script reads our `ae.fa` file every time we run it, but we know most programs don't work that way. The programs we used in bash expected a data file as an *argument*, and that's a good convention for programs we write too.\n",
-    "\n",
-    "In Python, our program can get these arguments, but we have to load a library to access them. Google it!\n",
-    "\n",
-    "`import sys`\n",
-    "\n",
-    "https://docs.python.org/3/library/sys.html\n",
-    "\n",
-    "Libraries are incredibly useful - there are libraries for working with numeric and scientific data, generating plots, fetching data from the web, working with image and document files, databases, etc. And of course, there's a library for getting things like your script's command-line arguments.\n",
-    "\n",
-    "So, let's change our `read_fasta.py` program slightly\n",
-    "\n",
-    "    import sys\n",
-    "    read_fasta(sys.argv[1])\n",
-    "\n",
-    "And run it. But what happens if we don't have a file name\n",
-    "\n",
-    "    if len(sys.argv) < 2:\n",
-    "        print 'Usage:', sys.argv[0], '<sequence.fa>'\n",
-    "        exit(1)\n"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -3186,7 +3181,7 @@
  "metadata": {
   "anaconda-cloud": {},
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
    "name": "python3"
   },
@@ -3200,7 +3195,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.7"
+   "version": "3.9.12"
   }
  },
  "nbformat": 4,