Consider refactoring `extract_deeppeptide_sequences.py`, `extract_plmutils_nucleotide_sequences.py`, & `scripts/run_nlpprecursor.py`

Arcadia-Science / peptigate

Peptigate ("peptide" + "investigate") predicts bioactive peptides from transcriptome assemblies or sets of proteins.

MIT License

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Consider refactoring `extract_deeppeptide_sequences.py`, `extract_plmutils_nucleotide_sequences.py`, & `scripts/run_nlpprecursor.py` #30

Open taylorreiter opened 5 months ago

taylorreiter commented 5 months ago

I refactored the functions read_fasta() and verify_translation() into utils.py. I also synced up variable names so they are consistent between scripts. However, the exact input of each function is slightly different based on differences in how predictions of amino acid sequences of peptides are reported, so I'd like to wait to refactor until we have testing in place (#29).