Extras for Harvard Class EPI511: Advanced Population & Medical Genetics

The EPI511.py file provided in the EPI511 class is a few years old. In contrast, the minihapmap.py file in this respository:

• reads the data files ~40 times faster
• makes it not painful to load all autosomal chromosome SNPs
• makes it easy to interactively load additional populations one at a time (each taking only a few seconds to load)
• makes it easier to explore and use all the chromosome and population data
• will use ~1.3GB of RAM if all 11 populations and all autosomal chromosomes are loaded
• is ~15 lines of code shorter
• demonstrates some good Python programming practices such as:
  • use class
  • avoid needing to modify the reusable file in order to use it
  • use pathlib.Path
  • avoid global variables

See example_usage.ipynb on how it is used.

If you have any questions, feel free to email castedo@castedo.com.