Position Frequency Matrix Featurizer

[tonydavis629]

Pull Request Template

Description

This PR adds a new featurizer PFMFeaturizer. This takes in a multisequence alignment and outputs a position frequency matrix. Utility function PFM_to_PPM converts the PFM to a position probability matrix and has been included in the PFMFeaturizer Module.

Also included is MSA_to_dataset in sequence_utils. This can be used to convert an MSA generated by the hhblits or hhsearch utilities into a dataset that can be read by PFMFeaturizer.

Testing is included for PFMFeaturizer, PFM_to_PPM, and MSA_to_dataset. Docs are updated as well.

Type of change

Please check the option that is related to your PR.

• 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)
  • In this case, we recommend to discuss your modification on GitHub issues before creating the PR
• 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

[tonydavis629]

Hm, any idea why biopython is not importing into the CI?

[arunppsg]

This should be in a try except block or SeqIO should be imported locally in a function where it is used

[arunppsg]

A couple of suggestions:

• undo d7c9d5b
• We need to place from Bio import SeqIO statement in a try-catch block or import SeqIO locally in a function. The reason why it is causing an error during import check is the workflow. In the workflow, for import check we install deepchem as pip install -e . which only installs the minimum install-requirements of deepchem, thereby excluding all auxiliary packages like PyTorch, Bio etc.
  

  deepchem/.github/workflows/common_setup.yml

  Line 32 in c606d52

  pip install -e .