added lectures 8 and 9

lectures/lecture08/README.md

@@ -1,6 +1,6 @@
-# Lecture 13
+# Lecture 08
 
-For our next set of lectures, we'll be heading back to Python to explore some specific tools common in computational biology research. Lecture 13 and 14 from Jesse Bloom will introduce you to the use of packages in general, and [Biopython](https://biopython.org) in particular, which includes many useful tools for manipulation and analysis of data related to molecular biology.
+For our next set of lectures, we'll be heading back to Python to explore some specific tools common in computational biology research. Lecture 08 and 09 from Jesse Bloom will introduce you to the use of packages in general, and [Biopython](https://biopython.org) in particular, which includes many useful tools for manipulation and analysis of data related to molecular biology.
 
 ## Learning objectives
 
@@ -14,12 +14,8 @@ After this section, you should be able to write Python functions that perform so
 
 ## Class materials
 
-- The content for this lecture is contained in the Jupyter notebook [lecture13.ipynb](lecture13.ipynb) located in this directory.
+- The content for this lecture is contained in the Jupyter notebook [lecture08.ipynb](lecture08.ipynb) located in this directory.
 
 - Please install [Biopython](https://anaconda.org/anaconda/biopython) prior to class by opening Terminal (Mac) or Anaconda Prompt (Windows) and executing the following code: `conda install -c anaconda biopython` . Alternatively (on either platform), open Anaconda Navigator, go to "Environments" and click "not installed". Search for biopython click the box to install.
 
 - This class requires use of Python 3.6+. If you installed Anaconda recently (e.g., within the last few months, since the start of the course), you should be fine. If you are working with an older installation of Python, please see [these instructions](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-python.html#updating-or-upgrading-python) for checking your version and updating if necessary.
-
-## Reminders
-
-- Homeworks 4 and 5 were due at noon on Thursday, November 7.

lectures/lecture08/lecture13.ipynb → lectures/lecture08/lecture08.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Lecture 13: Practical analyses in Python"
+    "# Lecture 08: Practical analyses in Python"
    ]
   },
   {
@@ -990,7 +990,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.7"
+   "version": "3.7.4"
   },
   "toc": {
    "nav_menu": {},
@@ -1010,5 +1010,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }

lectures/lecture09/README.md

@@ -1,4 +1,4 @@
-# Lecture 14: Practical analyses in Python
+# Lecture 09: Practical analyses in Python
 
 This lecture will continue using Python to perform biological sequence analyses.
 In particular, we will use [Biopython](https://biopython.org) to read in sequencing data.
@@ -16,12 +16,8 @@ After this lecture, you should be able to write Python functions:
 
 ## Class materials
 
-- The content for this lecture is containing in the Jupyter notebook [lecture14.ipynb](lecture14.ipynb) located in this directory. The content from lecture 13 is duplicated here for your convenience. 
+- The content for this lecture is containing in the Jupyter notebook [lecture09.ipynb](lecture09.ipynb) located in this directory. The content from lecture 08 is duplicated here for your convenience. 
 
 - If you have difficulty performing a `git pull` to obtain the materials for this class, it is likely because you have a conflict between `lecture13.ipynb` and the version in the public GitHub repo. You can resolve this by making a copy of that notebook (naming it something different, like `my_lecture13.ipynb`) and then discarding changes to the original notebook (you can do this in the GitHub Desktop app by going to the "Changes" tab, right clicking on this notebook, and selecting "Discard changes"). You should then be able to pull without issue.
 
 - Please also install [plotnine](https://plotnine.readthedocs.io/) prior to class by opening Terminal (Mac) or Anaconda Prompt (Windows) and executing the following code: `conda install -c conda-forge plotnine` . Alternatively (on either platform), open Anaconda Navigator, go to "Environments" and click "not installed". Search for plotnine and click the box to install.
-
-## Reminders
-
-- Homework 6 (Practical Python with biopython) is due on Tuesday, November 19 at noon, and includes material from lectures 13 and 14. Please see [this issue](https://github.com/fredhutchio/tfcb_2019/issues/35) for discussion of general questions about the class materials, and [this issue](https://github.com/fredhutchio/tfcb_2019/issues/34) for specific questions about homework 6. Kate will hold office hours for homework 6 on Monday, November 20 from 9-11 am in Arnold Atrium.

lectures/lecture08/lecture13and14.ipynb → lectures/lecture09/lecture09.ipynb

@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# Lecture 13: Practical analyses in Python"
+    "# Lecture 08 and 09: Practical analyses in Python"
    ]
   },
   {
@@ -1196,7 +1196,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.6.5"
+   "version": "3.7.4"
   },
   "toc": {
    "nav_menu": {},
@@ -1216,5 +1216,5 @@
   }
  },
  "nbformat": 4,
- "nbformat_minor": 2
+ "nbformat_minor": 4
 }