Hide BiopythonDeprecationWarnings when reading certain sequence files

[victorlin]

Description of proposed changes

Biopython 1.85 will show a deprecation warning when using format='fasta' with files that start with anything but '>'. This will be triggered in 2 cases:

1. when attempting to read GenBank files as FASTA
2. when attempting to read a FASTA file with comments

For (1), this deprecation warning will eventually become a ValueError which works with the existing try/catch block in ancentral.py to continue parsing as GenBank. For (2), it should be decided independently of Biopython if Augur should support FASTA with comments.

In both cases, the warning as-is should not be exposed to Augur users. It is not triggered when reading files format='fasta-pearson', so this is the easiest thing to do to maintain behavior of Biopython <1.85.

An alternative workaround is to suppress BiopythonDeprecationWarnings entirely with

warnings.simplefilter("ignore", BiopythonDeprecationWarning)

but that is less targeted and can lead to suppression of meaningful warnings.

Related issue(s)

Closes #1727

Checklist

• Automated checks pass
• Check if you need to add a changelog message
• Check if you need to add tests
• Check if you need to update docs
• Post-merge: create issue for deciding if Augur should support FASTA with comments

[victorlin]

This doesn't work on Biopython <1.85 because format='fasta-pearson' was only introduced with Biopython 1.85: biopython/biopython@378c4c1

[tsibley]

An alternative workaround is to suppress BiopythonDeprecationWarnings entirely with

warnings.simplefilter("ignore", BiopythonDeprecationWarning)

but that is less targeted and can lead to suppression of meaningful warnings.

You could use a more complex filter to more precisely ignore just the specific warning in question (e.g.)

[victorlin]

I'll open a new PR with warnings.filterwarnings along the lines of #1727 (comment)