Python

Animate a rotating protein from the Protein Data Bank
·870 words·5 mins
Python
Let’s make an animated gif of a rotating protein from PDB. This animation shows a human HLA-TCR complex (6py2). You’re looking at two human proteins: The HLA protein …
Build bioinformatics pipelines with Snakemake
·1458 words·7 mins
Python Tutorial
Snakemake is a Pythonic variant of GNU Make. Recently, I learned how to use it to build and launch bioinformatics pipelines on an LSF cluster. However, I had trouble understanding …
Join multiple PLINK dosage files into one file
·179 words·1 min
Python
If you have multiple PLINK dosage files and would like to merge them into one file, this script might save you some time.
Count the number of coding base pairs in each Gencode gene
·226 words·2 mins
Python
We can use Python to count the coding base pairs in each Gencode gene. Here, we report the base pair count by gene rather than by transcript. When we encounter different …
0-based and 1-based genomic intervals, overlap, and distance
·425 words·2 mins
Python
Here, I describe two kinds of genomic intervals and include source code for testing overlap and calculating distance between intervals.