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iqbal-lab-org / make_prg

Code to create a PRG from a Multiple Sequence Alignment file
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Feed gramtools + Fix #4 #5

Closed bricoletc closed 5 years ago

bricoletc commented 5 years ago

Hello rachel!

I'm adding support for nesting in gramtools and am looking to use your make_prg module as a dependency.

I'm proposing a few things here, please give me feedback on which ones you're not OK with and we can work together to (or I can) change again

1) Small changes to the command line interface: i've made it such that by default if you run the script again on the same MSA, it will overwrite the existing PRG. You can pass no-overwrite flag to avoid this. This makes it easier to debug interactively when you run several times 2) Did a refactoring of some functions into a utils.py module for ease of reading & modifying 3) The write_prg function writes the prg String using whitespace delimiters. I've added serialisation into a binary integer vector, which I read in gramtools. 4) I believe i've fixed #4 by sorting the variants inside get_interval_seqs function; i changed the tests accordingly (sort the variants in a site)

bricoletc commented 5 years ago

@rmcolq is this OK to merge?

rmcolq commented 5 years ago

Just reading through