Repo organization / cleanup

[trvrb]

A few points that could use cleanup / could be better organized:

1. I went to /data expecting to find sequence FASTAs, but instead only find ancillary data. Looking more it's clear that core sequence data is in dta/alignments/ and mascot_glm/alignments/. Rename /data to something more descriptive of move it to live in the appropriate analysis subdirectory.
2. Get ride of all the .DS_Store cruft. This should be listed in your .gitignore file. I see it is. Perhaps these snuck in before you added to .gitignore. You should just manually delete all these .DS_Store files from the repo now.
3. Similarly, manually delete all the .Rhistory files. Add .Rhistory to .gitignore.
4. Manually delete all the .ipynb_checkpoints/ directories.
5. sequence_information.zip is a complete duplicate of sequence_information/. Just delete the .zip file. Also rename sequence_information/ to sequence_acknowledgments. I expected "sequence information" to mean metadata.
6. out/ could be named something more informative. I can't tell what in here.
7. Add an repo organization overview to your top-level README file. https://github.com/blab/dengue-antigenic-dynamics and https://github.com/blab/global-migration are pretty good examples of this.
8. Add more intermediate READMEs to coach people through. The key places here are /dta and /mascot-glm. Again see https://github.com/blab/dengue-antigenic-dynamics/tree/master/titer_model or https://github.com/blab/global-migration/tree/master/geo for decent examples.
9. Ideally (but potentially more a stretch), provide a single .ipynb for each figure ala https://github.com/blab/adaptive-evolution/blob/master/adaptive-evolution-analysis/Figure1.ipynb

[miparedes]

@trvrb Thanks for these suggestions!

I've gone ahead and addressed 1-8 and have updated the main branch accordingly. I'll start working on #9 but it might take a bit of time. Given the time crunch to return to the editor sooner rather than later, I think the best course might be to do it while the editor revises the updated submission. Unless you think it's something that needs to be done before resubmitting?