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seb-mueller / chlamy_locus_map

Small RNA Locus Map for Chlamydomonas reinhardtii
GNU General Public License v3.0
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Cleaning up and location of output #14

Closed seb-mueller closed 5 years ago

seb-mueller commented 5 years ago

I've noticed there are multipe output directories, i.e. segmentation_2018, phasing and Plots within the github. Having many other projects, I'd like to streamline (so it's easy to understand instantly), could we agree on one output location if you don't object?

Since plots and other output tend to be large, I'd suggest to save outside the git repo to not clog it up to much, could we save everything in segmentation_2018 with some sort of version indication?

I could try to do this since I'd like to go through the code and clean/check it anyway making this sort of adaption along the way. Before I start I'd like to make sure you haven't go any changes left to add so I can start from the newest version?

nmatthews323 commented 5 years ago

Agreed! Let's get everything in segmentation_2018. The annotation will need re-running anyway so the only file which is in its final version at the moment is the segmentation.

seb-mueller commented 5 years ago

Brilliant! Hope you talk went smooth! One last thing, I was trying to move things around but some of the files are locked, could you run this quickly giving me access? I've done the same already:

chmod -R g+w /projects/nick_matthews
nmatthews323 commented 5 years ago

Hi Seb, should now be done, let me know if any issues!

seb-mueller commented 5 years ago

Update: I've cleaned up quite a bit, pleas let me know if I overdid it (details upon inspecting the commits). Effectively, I've chucked out all non used or obsolete files into archive, also from the base directory. I'm still not finished, but just wanted to let you know in case you want to have a look.

nmatthews323 commented 5 years ago

Heyyy, had a quick look and look generally sensible.

Re: counting biases are the objects required for repetativeness class actually in the local environment when running the annotation pipeline?: https://github.com/seb-mueller/chlamy_locus_map/blob/8a754a16638635c1ac01ea3d528b03e7157bb8d3/Scripts/chlamy_annotation_pipeline.R#L167

There's also a new empty function called processing biases in the source code, I'm assuming this is a working progress?

nmatthews323 commented 5 years ago

Just seen comment on other thread, let me know when you finished playing around with the counting biases and I'll give it a check through.

seb-mueller commented 5 years ago

Haha, you're ahead of time :) Yes, this line is gonna change (the rowSums are being precomputed in the gr object). I found it more sensible to have all parameter and path settings in one document..

seb-mueller commented 5 years ago

Pretty happy with the clean-up. One more thing might to put the 3 scripts from Key-coding-scripts into scripts the reduce folders, any objection? If not, I'll go ahead and close this issue.

nmatthews323 commented 5 years ago

All looks good to me! Key-coding-scripts was just the originals from back in 2016, we've pretty heavily adapted these now, and I have copies on my computer.