cdeitrick / lolipop Goto Github PK

We used lolipop in our poject, we found that the total frequency of genotypes in the last time point is larger than 100% (150), it is reasonable, there would be something wrong in the genotypy inference or clustering. Another question is one genotype is wrongly nested according to the isolate data, we can use the "-g" to calibrate it. While the frequency problem is still there.

The current version outputs a folder "scripts" that is empty. Previous versions had at least an r script here to allow easy alteration of ggmuller parameters. Would be nice to have that output again.

Minor changes are not difficult to add, but previous versions were able to be directly imported and processed.

-f and --frequencies both return the same error of "lolipop: error: unrecognized arguments"

I followed instructions to install - generating a conda environment for the required packages and installing lollipop through pip. I ran pip install lolipop --upgrade and lolipop lineage -h and all looked OK. When I tried running with an --input as my own CSV file the script broke. The cause of the problem seems to be FileNotFoundError: [Errno 2] No such file or directory: 'seaborn-white'

When installing lolipop (pip install lolipop, Python version 3.9) in a conda virtual environment on Ubuntu 22.04 LTS, I encountered an error when running the example data from the user guide. See error.txt for the detailed error message.
error.txt
Looking forward to your reply, thank you!

Lolipop should still work when one or zero mutation(s) are present and generate the same plots/tables. The plots and tables would obviously be empty/blank if there are no mutations.