Make a really cool script that everyone loves

raikens1 / mutation_rate

Code and raw data files for my work on private polymorphism differences between populations.

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Make a really cool script that everyone loves #9

Open raikens1 opened 7 years ago

raikens1 commented 7 years ago

Want to write a simple script that I can circulate that is user-friendly and well-documented so that anyone can do sequence context analysis.

\Throwing flowers

raikens1 commented 7 years ago

The python function in helper_code/get_context.py is not bad. Given a chromosome and position, it can look the context and return it as a string. It's cleaner than Varun's original and runs at about 4 times the speed when I tested it last. Some improvements could be made, always:

[ ] Add a main() function so that you can call it from the command line
[ ] only runs on the cluster because it uses the voightlab's hg19. Not sure what (if anything) to do about that.