data/microreact.pkl was not included in the poppunk installation. Added a line to MANIFEST.in to solve that.
running generate_visualisations() with cytoscape=True(which results in tree="none") and rank_fit=None resulted in UnboundLocalError: local variable 'rr_distMat' referenced before assignment
as none of the conditions to assign rr_distMat would be met in visualise.py. (self would be False, since update_db was set to False in assign mode). Solved this by removing condition and tree != "none" which was introduced recently.
Other issue not solved yet: using the --serial flag in assign mode does only add the query samples to the output (rather than all samples in the database as without that flag). For now I'll leave that turned off, but would be nice to get the full output despite this turned on.
Using v2.5 with beebop I encountered some issues:
data/microreact.pklwas not included in the poppunk installation. Added a line toMANIFEST.into solve that.cytoscape=True(which results in tree="none") andrank_fit=Noneresulted inUnboundLocalError: local variable 'rr_distMat' referenced before assignmentas none of the conditions to assignrr_distMatwould be met in visualise.py. (selfwould be False, sinceupdate_dbwas set to False in assign mode). Solved this by removing conditionand tree != "none"which was introduced recently.Other issue not solved yet: using the
--serialflag in assign mode does only add the query samples to the output (rather than all samples in the database as without that flag). For now I'll leave that turned off, but would be nice to get the full output despite this turned on.