search

LKremer / scbs

Python package with CLI for the analysis of single cell methylation data. Now known as MethSCAn: https://github.com/anders-biostat/MethSCAn
https://anders-biostat.github.io/MethSCAn/
GNU General Public License v3.0
11 stars 6 forks source link

pandas is faster than loadtxt #5

Closed alexey0308 closed 2 years ago

alexey0308 commented 3 years ago

this is a cherry pick from the csc PR, which is not related to matrix formats

LKremer commented 2 years ago

Hi Alexey,

I finally checked this one out, pandas is indeed much faster, which is a little surprising to me, but hey, cool! There is only one issue left, I think we need to add header=None to the pandas reader function, cause otherwise the first line will always be interpreted as a header, which it isn't. I'm just gonna merge and quickly add this myself.

Thanks for finding this performance upgrade!

alexey0308 commented 2 years ago

thanks for the update, it looks like you finished with the application part and finally got time for implementation :)