meng-ma-biomedical-ai / learning_python

README

Python is a general-purpose programming language that is very popular. I have wanted to learn Python for a long time but have put it off because I could get everything done in Perl and R. However, recently I've been working with Snakemake, which is a workflow management system based on Python, and realised that knowing Python would help me use the tool better. In addition, a lot of my colleagues are using Python, so it helps to be able read and write Python.

The Jupyter Notebook

The notebook formerly known as the IPython Notebook has also been on my list of things to learn. It serves as an interactive session for interweaving code and plain text. Just install Anaconda for your operating system and that will install Jupyter Notebook.

wget -c https://repo.anaconda.com/archive/Anaconda3-5.2.0-Linux-x86_64.sh
bash Anaconda3-5.2.0-Linux-x86_64.sh
source ~/.bashrc

After installation, run jupyter notebook to host an interactive session. I will use Jupyter notebooks to keep track of my Python code. Below are some useful links:

• Comprehensive Beginner’s Guide to Jupyter Notebooks for Data Science & Machine Learning

Shortcuts

Some shortcuts:

• The notebook has a command and edit mode; press escape to enter command mode and press enter to enter edit mode.
• In command mode, press m to change a cell to Markdown and y to change a cell to code
• Control+enter to execute code
• a and b to insert a cell above and below, respectively
• Vim shortcuts like dd and hjkl work in command mode

Docker

Jupyter Docker Stacks are a set of ready-to-run Docker images containing Jupyter applications and interactive computing tools. Use jupyter/scipy-notebook, which includes popular packages from the scientific Python ecosystem.

docker pull jupyter/scipy-notebook:latest

Running a container from this GitHub repository to access the notebook directory.

docker run -v "$PWD":/home/jovyan/work -p 8888:8888 jupyter/scipy-notebook:latest

Reticulate

The reticulate package provides a comprehensive set of tools for interoperability between Python and R. Reticulate embeds a Python session within your R session, enabling seamless, high-performance interoperability.

install.packages("reticulate")
library(reticulate)
use_python("/anaconda3/bin/python")

Check configurations

# check if Python is available
py_available()

# check Python config
py_config()

# check if module is available
py_module_available("umap")

# check version of Python to use with reticulate
# and location of module
py_discover_config("umap")

Using Python in R Markdown

```{python}
import sys
print(sys.version)
```

Links

• Perl to Python phrasebook for those coming from Perl and wanting to learn Python