Course material for the python beginner's course at the MPIMM Bremen
Course held by Niek Stortenbeker and Anna Mankowski on March 19th and 20th 2019.
Navigate to the day-1 or day-2 folder to find the materials of each day.
- introduction to python
- Visual QuickStart Guide Python - Toby Donaldson (available on mpg books)
- automate the boring stuff with python
- real python
- python data science handbook
- Bioinformatics with Python Cookbook - Tiago Antao (available on mpg books)
- numpy for simple descriptive statistics
- pandas for working with dataframes (like in R, or excel sheets). Very useful for all sorts of data analysis.
- arrow for working with dates
- re for regular expressions (a powerfull mini language for matching strings based on rules)
- pathlib for working with directories
- subprocess for excecuting command line programs from python
- biopython for bioinformatic tools
- matplotlib for plotting
- snakemake to make a smart command line programs workflow
- click basically a better argparse
- vim: simple command line editor
- atom: very nice text editor with syntax highlighting and other goodies
- PyCharm: an good integrated development environment. Basically this is a very smart text editor. (that might be a little more difficult to start using).
If you are looking for small projects to improve your python skills, here are a few examples:
- ignore case (use for instance .lower())
- print a warning when a name from the sample_names.csv is not used
- make the script rename all fasta files in a specified directory automatically (use pathlib!)
- only write the sequences that are in the table, ignore the other sequences (change the if statements)
- change the name in a way that the original name stays preserved (e.g. CBC2017_2738-Sample1)