Hide BiopythonDeprecationWarnings when reading certain sequence files

[victorlin]

Description of proposed changes

Biopython 1.85 shows a deprecation warning when using format='fasta' with files that start with anything but '>'.

The warning as-is should not be exposed to Augur users. It is not triggered when reading files with format='fasta-pearson', so this is the easiest thing to do continue accepting such files for Biopython >=1.85.

This way, Augur users get consistent, backwards compatible behavior no matter the Biopython version they use.

Related issue(s)

Fixes #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
• Merge base PR Centralize sequence read operations #1730

[corneliusroemer]

Suggestion for this elegant solution with version switch is from @tsibley: #1727 (comment)

[corneliusroemer]

A unit test testing that a variety of fasta's are supported would be cool maybe, we already know that our integration tests catch it, but not unit ones.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

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Additional details and impacted files

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