See #2700 for background, cross reference biopython/biopython#2833 (comment) e.g.

$ grep assertTrue *.py | grep "=="
common_BioSQL.py:        self.assertTrue(self.db.load(seqiter) == 1)
test_ClustalOmega_tool.py:        self.assertTrue(error.strip() == "" or
...

and:

$ grep assertFalse *.py | grep "!="
test_Restriction.py:        self

Hey,

I would propose extend list of available models by SeqVec (ELMo-based implementation) which was presented in the Modeling aspects of the language of life through transfer-learning protein sequences paper.

SeqVec model trained on UniRef50 is available at: [SeqVec-model](

This issue is a roadmap for Molly.jl development. Feel free to discuss things here or submit a PR. Bear in mind that significant refactoring will probably occur as the package develops.

Low hanging fruit

Want to get involved? These issues might be the place to start:

• Speedups to the code. Both on the level of individual functions and the overall algorithm. [Getting there]
• Look over

Actual test coverage is ~89%. That's great! However, would be great to increase that number to make this package more reliable and avoid future regressions ;)

It's easy to see what lines are missing tests using codecov and coveralls.

We need to find a way to test `MIToS