photon
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jdrudolph
AttributeError: 'NoneType' object has no attribute 'text'
Dear Jan,
Recently I have tried to get Photon up and running within Perseus and I started with the tutorial dataset that was posted here as well. The tutorial is very clear, so thanks for that!
However, when I get to the very last stage (Actually performing the Photon analysis) I get the following error:
Any help is greatly appreciated!
All the best (and stay healthy ;) Donna
Hi @DonnaOliviaD @chunxiaoren83 ,
I'm currently trying to disentangle which version of Perseus, perseuspy, and photon_ptm cause this issue. I contacted the Perseus developers and hopefully will be able to give you an update soon.
Best, Jan
Currently getting an almost identical problem at stage 4 of "Perform PHOTON analysis and visualize the results"; "Perform PHOTON analysis to obtain 'Signaling functionality scores' for all proteins in the network. (Network => Processing => Modifications => PHOTON). Select the Reconstruct signaling networks using ANAT option and enter ENSP00000265171 (ENSP id of EGF stimulus) as signaling source."
Selecting the Node and then Network => Processing => Modifications => Photon comes up with this window initially:
Trying to direct to the Photon python script file comes up with this error (whether or not I also select the Python executable)
EDIT: As an update - I ran through the tutorial again from the start with a fresh install of Perseus and Python (v3.9.1). I also followed along with the very useful tutorial @jdrudolph ran in 2018 that is available on YouTube (https://www.youtube.com/watch?v=KtKYktFGsEE), with the only differences being in Perseus version, Python version and the 9606 Protein Links txt file version. Error seems to be in loading the PHOTON script file correctly after clicking the PHOTON button under Network => Modifications => PHOTON.
If you have any suggestions on how to fix this issue or if anybody has any fixes that worked for them, I would very much appreciate hearing them.
