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genome-transformer's Issues

Incorporating Phylogeny

Tasks:

  • Extract phylogeny metadata from NCBI
  • Determine data organization for phylogeny with rest of metadata

Tokenizer and converting FASTAs

  • Use BioPython (or some other package) to write a function that parses FASTA files (check using data in Drive > Dry Lab > Research Development > FASTA data)
  • Add to tokenizer edge case

Hello!

This is great! Anyway I can help out? Are you all doing this for school or part of a lab?

Parsing Metadata

Tasks:

  • Read in and view the metadata
  • Understand how to work with metadata object
  • Define important pieces of the metadata relevant to positional embeddings
  • Summarize metadata on important sites for wet lab expertise (ie., histogram)

Make tokenizer for gene sequences

Create a tokenizer for base pairs of gene sequences.

  • Encode base pairs
  • Encode position of base pairs
    • With respect to sequence
    • With respect to transcription start site

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