Error in sanitise proteins step

[aebaci]

./filter_fastas_before_clustering.py -f /home/WorkKinfin/ACYPI.Acyrthosyphon_pisum.faa -p 0 -l 30 -s 0 File "./filter_fastas_before_clustering.py", line 33 print ">%s.%s\n%s" % (self.prefix, self.header, self.seq) ^ SyntaxError: invalid syntax

I get the same error when I try the example parallel code (but several times).

[aebaci]

Actually, I tried to run all of the .py of the scripts folder, and all of them give some SyntaxError. The init.py file is empty. I suppose that's not OK? But I ran the kinfin test it worked, so I'm not sure what's the problem.

[DRL]

Hey,

I made some changes, could you do git pull in the kinfin folder and try again?

cheers,

dom

[aebaci]

Hi Dominik:

Thank you for your fast reply! (never expected it). I did the git pull and it modified 12 files (I think all the .py). I reran the test and it worked.

I tried again the parallel -j1 '~/kinfin/scripts/filter_fastas_before_clustering.py {} > {/.}.sl.faa' ::: /home/antonella/WorkKinfin/*faa This time I didn't get an error message, but it did show the following message for each fasta, and produced empty files with .sl.faa in the directory: usage: filter_fastas_before_clustering.py -f FILE [-p INT] [-l INT] [-s INT] [-h|--help] I tried the option without parallel with one of the fastas, ./filter_fastas_before_clustering.py -f ~/WorkKinfin/ACYPI.Acyrthosyphon_pisum.faa -p 0 -l 30 -s 0 > ~/WorkKinfin/proteomeskin/ACYPI.Acyrthosyphon_pisum.sl.faa and it worked!

Maybe I was missing or had an error in the use of the parallel example? It is my first time using it.

I will continue the pipeline and will write if I find any more issues.

Thanks!

El mié, 27 mar 2024 a las 10:59, Dominik R Laetsch (< @.***>) escribió:

Hey,

I made some changes, could you do git pull in the kinfin folder and try again?

cheers,

dom

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[DRL]

Cool. Glad I could help.

In the parallel command the -f was missing. Kinfin gets confused when there is no -f. This command should work.

parallel -j1 '~/kinfin/scripts/filter_fastas_before_clustering.py -f {} > {/.}.sl.faa' ::: /home/antonella/WorkKinfin/*faa

Will close this issue now and if more things come up you just keep opening new issues.

cheers,

dom