[BUG] Pandas error in `anvi-get-codon-frequencies`

[philipwoods]

Short description of the problem

When running anvi-get-codon-frequencies, there is a TypeError in how pandas is used in _make_gene_codon_frequency_table.

anvi'o version

Anvi'o .......................................: marie (v8)
Python .......................................: 3.10.13

Profile database .............................: 38
Contigs database .............................: 21
Pan database .................................: 16
Genome data storage ..........................: 7
Auxiliary data storage .......................: 2
Structure database ...........................: 2
Metabolic modules database ...................: 4
tRNA-seq database ............................: 2

System info

The operating system is Red Hat enterprise Linux. Anvi'o was installed in a conda environment.

Detailed description of the issue

When running anvi-get-codon-frequencies I get the following error:

Traceback (most recent call last):
  File "/export/data1/sw/anaconda3-2019.07/envs/anvio-8/bin/anvi-get-codon-frequencies", line 420, in <module>
    main(args)
  File "/export/data1/sw/anaconda3-2019.07/envs/anvio-8/bin/anvi-get-codon-frequencies", line 115, in main
    frequency_df = multigenome_codon_usage.get_frequencies(
  File "/export/data1/sw/anaconda3-2019.07/envs/anvio-8/lib/python3.10/site-packages/anvio/codonusage.py", line 2265, in get_frequencies
    frequency_df = next(frequency_table_generator)
  File "/export/data1/sw/anaconda3-2019.07/envs/anvio-8/lib/python3.10/site-packages/anvio/codonusage.py", line 2281, in _get_genome_frequency_table
    genome_codon_usage = SingleGenomeCodonUsage(
  File "/export/data1/sw/anaconda3-2019.07/envs/anvio-8/lib/python3.10/site-packages/anvio/codonusage.py", line 89, in __init__
    self._make_gene_codon_frequency_table()
  File "/export/data1/sw/anaconda3-2019.07/envs/anvio-8/lib/python3.10/site-packages/anvio/codonusage.py", line 231, in _make_gene_codon_frequency_table
    gene_codon_frequency_df = gene_codon_frequency_df[constants.codon_to_AA]
  File "/export/data1/sw/anaconda3-2019.07/envs/anvio-8/lib/python3.10/site-packages/pandas/core/frame.py", line 4051, in __getitem__
    check_dict_or_set_indexers(key)
  File "/export/data1/sw/anaconda3-2019.07/envs/anvio-8/lib/python3.10/site-packages/pandas/core/indexing.py", line 2783, in check_dict_or_set_indexers
    raise TypeError(
TypeError: Passing a dict as an indexer is not supported. Use a list instead.

[meren]

I see a lot of pandas errors reported lately. I wonder if there was an update recently that causes all these incompatibility issues.

Note for self: we should always finalize requirements.txt with explicit version numbers prior to release :(

[xvazquezc]

Fwiw, I'm running 2 recent installations of anvio-dev in Ubuntu and Rocky Linux, both with pandas=1.4.4 and I haven't had any issues. (I even ran anvi-get-codon-frequencies in case it was a program-specific issue; no errors either).

I see a pretty old anaconda install, from when the flexible solve for environment deps was the default - less painful, but more prone to environments not being properly set.

[philipwoods]

For what it's worth, I can verify that pandas 1.4.4 is installed in the environment:

(anvio-8) [pwoods@ocean revision]$ conda list | grep pandas
pandas                    1.4.4                    pypi_0    pypi

[meren]

This is very interesting. @philipwoods, would you consider sharing your contigs-db file and the exact command you're running on it to get this error? Maybe we can try to reproduce it on our end and see if we can solve it.

[philipwoods]

I get the error while running anvi-get-codon-frequencies -c ANME-2a_sp._Agg-19359.db -o test.txt with the attached contigs database. ANME-2a_sp._Agg-19359.zip

[philipwoods]

I just finished installing an anvio-dev environment and the command above ran with no issue, which is confusing but possibly also useful debugging information.