escapepod 0.6.2

Fast Python reader/writer for Oxford Nanopore POD5 files, backed by a pure Rust engine

escapepod

Fast Python reader/writer for Oxford Nanopore POD5 files, backed by a pure Rust engine (the same engine as the escpod CLI). It mirrors the API of Oxford Nanopore's official pod5 package closely enough to be a mostly drop-in replacement, while reading and writing considerably faster.

Alpha quality and under active development. APIs and output formats may change without notice. Verify results against the official ONT pod5 tools before relying on it for anything important.

Install

pip install escapepod

Wheels are published for CPython 3.9+ (abi3) on Linux (x86_64/aarch64, manylinux + musllinux) and macOS (x86_64/arm64).

Usage

import escapepod

with escapepod.Reader("experiment.pod5") as reader:
    print(f"{reader.read_count} reads")
    for read in reader:
        signal = reader.get_signal(read)          # raw ADC (int16)
        print(read.read_id, read.num_samples, signal.mean())

See the documentation for the full API.

License

MIT