Brilliant, that's worked perfectly! Thanks!
I'm new to bioinformatics, and am learning to use g:profiler. I'm using a terminal on a mac. The advice I got was:
Install the client.
pip install gprofiler-official #this works fine, and says "Requirement already satisfied"
Get help on the client parameters.
gprofiler_cli.py --help
the output I get is:
$ gprofiler_cli.py --help -bash: gprofiler_cli.py: command not found (base)
Example run from the documentation.
gprofiler_cli.py -o scerevisiae "swi4 swi6"
the output I get is:
$ gprofiler_cli.py -o scerevisiae "swi4 swi6" -bash: gprofiler_cli.py: command not found (base)
I'd be grateful for any help as I'm stuck, despite reading around the internet Thanks!
1 answer
Hi!
g:Profiler had a major update earlier this year that deprecated the use of gprofiler_cli.py.
To make gprofiler_cli.py work again, I'd recommend uninstalling gprofiler-official and reinstalling the 0.3.5 version.
pip uninstall gprofiler-official
pip install gprofiler-official==0.3.5
The caveat is that the data behind gprofiler-official version 0.3.5 is not getting updates anymore. Generally we recommend using the latest version of gprofiler-official as a python client or the gprofiler2 R package (https://CRAN.R-project.org/package=gprofiler2). We don't currently have a command line tool for accessing g:Profiler.
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