Intro to IPython Notebooks

Transcription

1 Intro to IPython Notebooks for the Bioinformatics group 17 July 2014 Stace Beaulieu, WHOI Ocean Informatics Coordinator projects/ocean informatics working group/ This is a "lightweight" workflow software that you can use to run your bash scripts and python scripts all together from one interface. These notebooks are also easy to share with others. Goals of the workshop: kh Introduce you to IPython Notebooks You will create your own Notebook to process a fasta file that Ann provided You will download a helpful Notebook for the biopython software package

2 The 3 software packages that you will need are: Bash shell (default on Mac, need to install on Windows) Anaconda python 2.7 (Please install this, even if you already have python running on your computer. This package includes the IPython Notebook software.) (note: large file 300 MB) biopython (This is not included in the Anaconda package, and we need it.) 1. Windows only: Git Bash Install Git for Windows by download and running the installer. This will provide you with both Git and Bash in the Git Bash program. Mac only: Bash The default shell in all versions of Mac OS X is bash, so no need to install anything. You access bash from the Terminal (found in /Applications/Utilities). 2. Python: Download and install Anaconda CE / h Use all of the defaults for installation except make sure to check Make Anaconda the default Python. 3. After installing Anaconda (and Git Bash for Windows), make sure that you can open IPython Notebook software: Open shell (e.g., Git Bash) or Anaconda command prompt Type "ipython notebook" enter at shell prompt Wait a few seconds, and a web browser should open. 4. Next, to install biopython: Open the Anaconda command prompt Type "pip install biopython (or, this should work, too: conda install biopython )

3 Note: if the link to Google Drive does not work, and you are interested in trying out IPython Notebooks, please contact Stace Beaulieu 5. Also, copy from Google Drive a directory for today's class: folder "for_bash_biopython" 5 files: DE_targets.txt, fatty_stats.sh, Targets.py, Trinty.fasta (note: large file 200 MB), Python_ESIP_SWC.ipynb (this was not in original ; we can type into the Notebook cells)

4 Introduce you to IPython Notebooks: How didi get hooked? Homepage for IPython Notebook: Fernando Perez, keynote address at 2013 SciPy Conference: (nice history, plus vision for the future) Local Woods Hole user s group: WhyThon Rich Signell s (USGS Woods Hole) IPython Notebooks: usgs/notebook ECO OP project in collaboration with NEFSC: View IPython Notebooks as HTML webpages and download code: gallery of interesting IPython Notebooks 3:15

5 Introduce you to IPython Notebooks Let s try it out! Open shell (e.g., Git Bash) Navigate to the folder in which you stored today s files from Google Drive Type "ipython notebook" enter at shell prompt Wait a few seconds, and a web browser should open. Open a new notebook (or, open the file Python_ESIP_SWC.ipynb if you downloaded this) Type into the first cell, and hit shift enter Click on + button to add a new cell, type 2 5 and hit shift enter Cll Cell > All output t> Clear Cell > Run All Add a new cell, do List Exercise from Software Carpentry

6 Introduce you to IPython Notebooks Let s try it out! [Copy code for one of these to clipboard] Add a new cell, paste the code from clipboard, hit shift enter Note: to plot in the Notebook itself, first type at the top of the cell: %pylab inline For more basics of Ipython Notebook: data intro/core/notebook.html For more basics of Python programming: carpentry.org/v4/python/index.html 3:30

7 You will create your own Notebook to process a fasta file that Ann provided: This is why we are here Open a new Notebook (or, continue by adding new cells to your current Notebook) (Stace will open a prepared Notebook: Stace_for_bioinformatics_group.ipynb ) Make sure you are in the correct working directory with the bash script, python script, and input fasta file Runbash script Run python script Check output fasta file 3:40

8 You will create your own Notebook to process a fasta file that Ann provided: Now, let s put all the scripting into the Notebook We will open the bash script and the python script in a text editor and copy/paste into new cells (but you can also load the text file right into the cell, e.g., %load "Targets.py ) Save your Notebook file using File > Download as > *.ipynb (note this is in JSON data format) 3:50

9 This is what it looks like

10 You will download a helpful Notebook for the biopython software package Download and interact with a Notebook from nbviewer: Google nbviewer biopython notebook/blob/master/notebooks/02%20 %20Quick%20Start.ipynb b/ / b k /02%20 %20Q k%20s i b (Windows) Right click on upper right 'download notebook' to save.ipynb file to directory with Ann's files When you open the Notebook, it is executed, showing you all output. You can clear all cells and run the Notebook yourself. See how some cells just look like text? Show how cells can be code, markdown, or header.

11 Future Using Wakari reproducible science with just a browser: 16min: Y5GfuhCvStxgbynFNrxr3VFog&index=86 4:00