Small fixes for beebop #217
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
johnlees
approved these changes
Sep 7, 2022
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
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 assign
rr_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.