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jbloomlab / dms_tools2

software for the analysis and visualization of deep mutational scanning data
GNU General Public License v3.0
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Output `bcInfo` in `.csv` #41

Closed khdcrawford closed 4 years ago

khdcrawford commented 4 years ago

It would make downstream analyses more flexible if the final output containing the barcode info from dms2_bcsubamp was in .csv format.

https://github.com/jbloomlab/dms_tools2/blob/d658fed9ef7410f1cfda7b31c8cdc38b3e29cf87/scripts/dms2_bcsubamp#L40-L48

jbloom commented 4 years ago

I'm fine with adding this change, although note that it's not exactly clear how the currently returned data is converted to CSV since some things (like R1 reads) are lists.

But if you want to make a change like this, I would suggest adding an additonal option like --bcinfo-csv to the program and making it return the file in the format you want?

khdcrawford commented 4 years ago

Sounds good. I agree with making it an option. I'll think on it a bit, but it seems most people just use the consensus for downstream analyses. I think my plan would be to just include the number of R1 and R2 reads, rather than the lists of those reads, that go into making the consensus

khdcrawford commented 4 years ago

I made a local branch of dms_tools2 and added a bcinfo_csv option, but I'm not sure how developing dms_tools2 is supposed to work, so am not sure how to proceed.

I also ran into issues with already having dms_tools2 installed locally, and the tests always using that instead of my edited version, so I wasn't able to fully test, but I did a couple small tests that seemed to work. Perhaps we can discuss when we meet next week.

jbloom commented 4 years ago

If you think your version is ready, just do the same thing we did for alignparse. Push your changes to a branch and then initiate a pull request. Make sure you have some sort of small test for what you added.

If you have local installs, you should be able to remove them all with ~/.local and then do python setup.py develop --user to install the development version in ~/.local.

Note that if you are running command-line programs rather than python imports, you also need this line at the end of your ~/.bashrc:

PATH="$HOME/.local/bin:$PATH"

See the Developing Python software locally instructions for the BloomLab conda environment.

jbloom commented 4 years ago

Addressed by pull request #42