Clinker usage about clinker HOT 9 CLOSED

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

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Hi @EmaBoni, I haven't tried using clinker inside a Jupyter notebook before so I'm not exactly sure about that - from what you've listed there it looks like the command should be correct. Would it be possible to post the full error log from when you try to run the program inside the notebook or in the command line?

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Hello @gamcil , thank you for your answer!
Here is the full attempt from the command line (NB: it is windows command line, not linux, might this be an issue?).
(Clinker) is my python environment created with Anaconda Navigator

`(Clinker) C:\Users\Emanuele Boni\clinker>python

Python 3.8.13 | packaged by conda-forge | (default, Mar 25 2022, 05:59:00) [MSC v.1929 64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.

import clinker
clinker

<module 'clinker' from 'C:\Users\Emanuele Boni\clinker\clinker\init.py'>

import os
os.listdir('C:\Users\Emanuele Boni\clinker\examples')

['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']

clinker 'C:\Users\Emanuele Boni\clinker\examples\*' -p

File "", line 1
clinker 'C:\Users\Emanuele Boni\clinker\examples\*' -p
^
SyntaxError: invalid syntax

clinker 'C:\Users\Emanuele Boni\clinker\examples'+'/' -p
File "", line 1
clinker 'C:\Users\Emanuele Boni\clinker\examples'+'/' -p
^
SyntaxError: invalid syntax

clinker examples/* -p
File "", line 1
clinker examples/* -p
^
SyntaxError: invalid syntax`

NB: the '^' arrow points at the first character after clinker

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Ah you are trying to run clinker from within the Python interactive shell, which is then recognising it as invalid syntax (since it isn't Python code). clinker should be run just from the command line itself - try exiting the Python shell and running the exact same command, e.g. clinker 'C:\Users\Emanuele Boni\clinker\examples\*' -p and it should work.

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This clarifies a lot, thank you!
I managed to run the pipeline on the examples (resulting image is as expected) and on my files. This is what I get:

I am a bit uncertain about the result because I expected the sequences to have much higher identity (more groups matching, higher identity percentage for the group that is correctly recognized). The alignment is done on the protein sequences, is that correct?
I will double check the gene sequences to make sure there are no errors there.
Any idea of other things that I am not considering when aligning these two files?

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Yes the alignments are done on the protein sequences - however if they are missing, clinker will try to translate the regions corresponding to gene/CDS coordinates in the input file. Not sure what is causing the issue in your case, would you be able to upload your files?

from clinker.

Ok! Yes, protein sequences are annotate in my files.
Here are the two files that I am using:
EBoni.zip

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Thanks a lot for your time and for your help!

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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:

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