SeqPro (Sequence processing toolkit)

import seqpro as sp

SeqPro is a Python package for processing DNA/RNA sequences, with support for protein sequences. SeqPro is fully functional on its own but is heavily utilized by other packages including SeqData, MotifData, SeqExplainer, and EUGENe.

All functions in SeqPro take as input a string, a list of strings, a NumPy array of strings, a NumPy array of single character bytes (S1), or a NumPy array of one-hot encoded sequences (uint8). Variable-length sequence collections are supported via the seqpro.rag submodule (Ragged arrays). There is also experimental integration with XArray through the seqpro.xr submodule.

Computational bottlenecks or code that is impossible to vectorize with NumPy alone are accelerated with Numba (e.g. padding sequences, one-hot encoding, decoding) and Rust via PyO3/maturin (e.g. k-mer shuffling).

Installation

pip install seqpro

API

N = 2
L = 9

# Generating random sequences
seqs = sp.random_seqs(shape=(N, L), alphabet=sp.DNA, seed=1234)

# Padding
sp.pad_seqs(seqs, pad="right", pad_value="N", length=12, length_axis=-1)

# One-hot encoding and decoding (via alphabet)
ohe = sp.DNA.ohe(seqs)
sp.DNA.decode_ohe(ohe, ohe_axis=-1, unknown_char="N")

# Tokenization
token_map = {"A": 7, "C": 8, "G": 9, "T": 10, "N": 11}
tokens = sp.tokenize(seqs, token_map=token_map, unknown_token=11)
sp.decode_tokens(tokens, token_map=token_map)

# Reverse complement (via alphabet or standalone)
sp.DNA.reverse_complement(seqs)
sp.reverse_complement(seqs, alphabet=sp.DNA)

# k-let preserving shuffling
sp.k_shuffle(seqs, k=2, length_axis=1, seed=1234)

# Calculating GC or nucleotide content
sp.gc_content(seqs, alphabet=sp.DNA)
sp.nucleotide_content(seqs, alphabet=sp.DNA)

# Randomly jittering sequences
sp.jitter(seqs, max_jitter=2, length_axis=1, seed=1234)

# Collapse coverage to a given bin width
sp.bin_coverage(coverage, bin_width=128, length_axis=1, normalize=False)

# Translation: DNA/RNA → amino acids
cds = sp.random_seqs(shape=(N, L), alphabet=sp.DNA, seed=42)
aa = sp.AA.translate(cds)

# One-hot encode amino acids
aa_ohe = sp.AA.ohe(aa)
sp.AA.decode_ohe(aa_ohe, ohe_axis=-1, unknown_char="X")

Alphabets

SeqPro ships three built-in alphabets:

Object	Type	Description
sp.DNA	NucleotideAlphabet	ACGT with reverse complement support
sp.RNA	NucleotideAlphabet	ACGU with reverse complement support
sp.AA	AminoAlphabet	Standard 20 amino acids + stop codon (*), with codon translation

Each alphabet exposes .ohe(), .decode_ohe(), and .reverse_complement() (nucleotide alphabets) or .translate() (amino acid alphabet) directly on the object.

More to come!

All contributions, including bug reports, documentation improvements, and enhancement suggestions are welcome. Everyone within the community is expected to abide by our code of conduct