example_analysis.py failure

[josephwb]

I personally find python errors very difficult to track down. Do you have any idea what is going on?

$ python3 example_analysis.py 
Workflow runs with 8 threads.
REMEMBER TO UPDATE THE NCBI DATABASES REGULARLY! Looks like you last updated it 3 days ago.
Run the file 'update_databases.py' from the data folder to automatically update. Note, that you are accessing a US government website to do so.
Translate input names to ncbi taxonomy...
Build table with information about sequences and taxa.
Initialize NODES and NAMES!!
Load sequences...
Begin update: 2021-04-08 16:21:16.862005.

Clean the input data: data/tiny_test_example/test.tre, data/tiny_test_example/test.fas.Format mrca: {18794} - SenecioBlast round number 0. Max. rounds set to 1.
Find new sequences using the BLAST database.
Blast 1 out of 5, subsample size is 1.
Warning: [blastn] Number of threads was reduced to 4 to match the number of available CPUs
Blast 2 out of 5, subsample size is 1.
Warning: [blastn] Number of threads was reduced to 4 to match the number of available CPUs
Blast 3 out of 5, subsample size is 1.
Warning: [blastn] Number of threads was reduced to 4 to match the number of available CPUs
Blast 4 out of 5, subsample size is 1.
Warning: [blastn] Number of threads was reduced to 4 to match the number of available CPUs
Blast 5 out of 5, subsample size is 1.
Warning: [blastn] Number of threads was reduced to 4 to match the number of available CPUs
Length of new seqs before filtering: 52
Traceback (most recent call last):
  File "example_analysis.py", line 17, in <module>
    test.run(status_end=1) # status ends limits the number of blast rounds
  File "/home/josephwb/Downloads/PhylUp/PhylUp/phyl_up.py", line 463, in run
    new_seqs = self.call_filter(new_seqs, self.aln)
  File "/home/josephwb/Downloads/PhylUp/PhylUp/phyl_up.py", line 303, in call_filter
    new_seqs = self.compare_filter(new_seqs)
  File "/home/josephwb/Downloads/PhylUp/PhylUp/phyl_up.py", line 341, in compare_filter
    f.filter(new_seqs, self.config.downtorank)
  File "/home/josephwb/Downloads/PhylUp/PhylUp/phyl_up.py", line 783, in filter
    if all_preferred.index == True:
ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()

[mkandziora]

Ha, yes. Pandas error. Thanks for the patch. In theory, both (any() and all()) should work, just from the logic any() is more appropriate here. Fix added.