seqpro

Python/Rust package for fast biological-sequence processing. Python+NumPy+Numba for hot loops, a small Rust extension (src/kshuffle.rs) for graph-algorithm ops, and a Rust-native Ragged array (_core.Ragged) for variable-length batches. Imported as import seqpro as sp.

When to use

• Encoding/decoding DNA, RNA, or protein sequences (OHE, integer tokens, padding).
• Sequence augmentation: reverse complement, k-mer shuffle, jitter, random draws.
• Sequence stats: GC content, nucleotide composition, length.
• Variable-length batches (e.g. peaks, transcripts of different sizes) → sp.Ragged.
• Genomic interval I/O: sp.bed, sp.gtf.

Conventions (load these into working memory)