Closed johnlees closed 2 years ago
if type(top_value) == str:
sketch_dict = json.loads(top_value)
else:
sketch_dict = top_value
@nickjcroucher Would you be able to confirm the MST -> phylogeny is still working as expected here?
Example for the merged clusters
Reference database: /media/mirrored-hdd/shorsfield/jobs/poppunk-models/Salmonella/sal_sketch40k
Model fit: /media/mirrored-hdd/shorsfield/jobs/poppunk-models/dbscan_indiv_refine_both
query file: /media/mirrored-hdd/shorsfield/jobs/poppunk-models/Salmonella_query_popPUNK_ids_split.txt.acaaae
command: poppunk_assign --db sal_sketch40k --query Salmonella_query_popPUNK_ids_split.txt.acaaae --model-dir dbscan_indiv_refine_both --core --threads 20 --output query-assignments_acaaae --qc-filter prune
@nickjcroucher Would you be able to confirm the MST -> phylogeny is still working as expected here?
Apologies for the delay - for a bacterial example, ape
says they are identical, consistent with visual inspection:
v2.4.6
:
v2.5.0
:
Great, thanks Nick!
wrt cytoscape issues
When trying to just create cytoscape output for a subset of the data, instead of not subsetting at all like happened on the command line, this time I get "IndexError: list index out of range" for this isolate_names[n]. I checked what these objects there store, and actually isolate_names and viz_subset are holding the same list of samples (the subset I am looking for). If I understand the code correctly, isolate_names should rather have all isolate names rather that just the subset, right? Since isolate_names is coming from combined_seq again, is the cause of this problem that I run it with rank_fit = None/tree = "nj"?
Just need to have a look at that stall, which may be a sketchlib issue
🤯
Fastastic!
Todo:
tree = None
in cytoscape visualisations.combined_seq
not set here--api-key
option to visualisation.microreact
file10050_2#1
)~ couldn't replicate