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netZoo / netZooPy

netZooPy is a network biology package implemented in Python.
https://netzoo.github.io/
GNU General Public License v3.0
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LIONESS Py error #335

Closed wilsonavac closed 8 months ago

wilsonavac commented 8 months ago

I am running lioness with cli like this:

netzoopy lioness -e /home/ubuntu/partial_expression.tsv -m /home/ubuntu/whole_blood_tissues_motif.txt -p /home/ubuntu/whole_blood_tissues_ppi.txt -op /home/ubuntu/copdgene_yes_cp_dev_panda_lion.txt -ol /home/ubuntu/yes_copd_dev_lion/ --computing gpu --panda_start 1 --panda_end 5 --precision single --save_memory --mode_process intersection --save_single_lioness --ignore_final

And I am getting this error:

File "/opt/conda/lib/python3.10/site-packages/netZooPy/lioness/lioness.py", line 135, in init self.export_panda_results = obj.export_panda_results AttributeError: 'Panda' object has no attribute 'export_panda_results'. Did you mean: 'save_panda_results'?

can you please help me :)

violafanfani commented 8 months ago

Hi @wilsonavac! This is the issue with --save_memory that doesn't keep the data from PANDA, hence the error in lioness. Try running it without the save memory flag, it should work. I will work on a fix, this should not be happening/ you shouldn't have access to that flag.

Let me know if this works. Viola

violafanfani commented 8 months ago

The LIONESS docs are now explaining how to use the CLI better. Will need to remove --save-memory flag from CLI

violafanfani commented 8 months ago

The flag is now removed with #340