Clinker usage

Sorry for the dumb question, I am trying to use clinker but I cannot analyze files within a folder.

I have cloned clinker from git and installed it via pip, as indicated in the readme, so now I have a clinker folder that includes the examples. I have created a dedicated environment and I am working in Jupyter notebook. This is the code that I am using:

import sys sys.path.append('C:\\Users\Emanuele Boni\clinker') import clinker import os proj_dir = 'C:\\Users\Emanuele Boni\clinker\examples' os.listdir(proj_dir)

This returns the content of the folder as ['A. alliaceus CBS 536.65.gbk', 'A. burnettii MST-FP2249.gbk', 'A. mulundensis DSM 5745.gbk', 'A. versicolor CBS 583.65.gbk', 'note.md', 'P. vexata CBS 129021.gbk']

However, if I try to run clinker proj_dir/* -p I get the error message SyntaxError: invalid syntax pointing at proj_dir

I have tried several things: creating a subfolder in the folder where I am running the notebook, writing the folder name as string and as variable (with and without quotes), running the lines of code directly from the command line instead of inside the notebook. None of these worked. I think I am not considering something very trivial, but I cannot figure out what it is.

Thank you for your help and for developing this tool! Emanuele

[EmaBoni]

Thanks a lot! We found 18-19% identity threshold was ideal for us. You have been extremely helpful, thanks again for your time and for this very useful tool! Kind regards, Emanuele

[gamcil]

Just had some time to have a look at this. It seems the files are read in correctly (it is picking up the AA translations just fine), but the alignments are falling below the default identity threshold (30%) and so are getting filtered out. You can lower this threshold using the -i/--identity argument, e.g. clinker EBoni/*.gb -i 0.2 -p. That command gives me this: