sequence_utils for sequence homology search

[tonydavis629]

Pull Request Template

Description

This PR adds two wrapper functions for hhsearch and hhblits, from the protein homology search tool hhsuite. Currently runs by saving output files to the disk, future work is needed to featurize the multisequence alignment output to produce a probability frequency matrix. Unit testing, documentation and tutorial update is included. Example database files necessary for unit tests are added in utils/test/data. Mac and linux requirements are updated to reflect the new dependency, hhsuite is not supported on windows.

Type of change

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• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
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• Documentations (modification for documents)

Checklist

• My code follows the style guidelines of this project
  • Run yapf -i <modified file> and check no errors (yapf version must be 0.22.0)
  • Run mypy -p deepchem and check no errors
  • Run flake8 <modified file> --count and check no errors
  • Run python -m doctest <modified file> and check no errors
• I have performed a self-review of my own code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• I have added tests that prove my fix is effective or that my feature works
• New unit tests pass locally with my changes
• I have checked my code and corrected any misspellings

[arunppsg]

This bioconda can probably be removed since hhsuite is only included in env_mac.yml and env_ubuntu.yml and having bioconda there will be sufficient.

[tonydavis629]

Ok there the CI goes! Strange. Thanks @arunppsg I made that change.

[rbharath]

Did a review and LGTM