Experimental library for interacting with POD5 files using the Rust programming language. This repository provides multiple crates covering different portions of the POD5 file format and APIs for reading and writing.
use std::{fs::File, path::PathBuf, error::Error};
use pod5::{self, reader::Reader};
fn run() -> Result<(), Box<dyn Error>> {
let path = "../extra/multi_fast5_zip_v3.pod5";
let file = File::open(path)?;
let mut reader = Reader::from_reader(file)?;
let calibration = reader.read_dfs()?.into_calibration();
let signal_df = reader.signal_dfs()?.flatten().next().unwrap();
println!("{:?}", signal_df.to_picoamps(&calibration));
Ok(())
}Output:
SignalDataFrame(shape: (22, 3)
┌─────────────────────────────────┬─────────────────────────────────┬─────────┐
│ read_id ┆ signal ┆ samples │
│ --- ┆ --- ┆ --- │
│ str ┆ list[f32] ┆ u32 │
╞═════════════════════════════════╪═════════════════════════════════╪═════════╡
│ 0000173c-bf67-44e7-9a9c-1ad0bc… ┆ [68.796082, 68.620575, … 64.75… ┆ 102400 │
│ 0000173c-bf67-44e7-9a9c-1ad0bc… ┆ [65.110573, 74.587585, … 58.61… ┆ 21227 │
│ 002fde30-9e23-4125-9eae-d112c1… ┆ [111.618126, 67.567574, … 66.1… ┆ 37440 │
│ 006d1319-2877-4b34-85df-34de72… ┆ [101.263618, 68.971581, … 70.2… ┆ 102400 │
│ 006d1319-2877-4b34-85df-34de72… ┆ [73.359085, 69.673576, … 66.33… ┆ 102400 │
│ … ┆ … ┆ … │
│ 008ed3dc-86c2-452f-b107-6877a4… ┆ [103.194115, 54.580563, … 60.1… ┆ 14510 │
│ 00919556-e519-4960-8aa5-c2dfa0… ┆ [93.541603, 91.611107, … 73.35… ┆ 9885 │
│ 00925f34-6baf-47fc-b40c-22591e… ┆ [82.660591, 64.057571, … 72.30… ┆ 102400 │
│ 00925f34-6baf-47fc-b40c-22591e… ┆ [60.723068, 64.057571, … 70.72… ┆ 33970 │
│ 009dc9bd-c5f4-487b-ba4c-b9ce7e… ┆ [98.280113, 60.723068, … 52.65… ┆ 15643 │
└─────────────────────────────────┴─────────────────────────────────┴─────────┘)
The crates will eventually be added to crates.io. To use any of these crates now, you can use cargo's git parameter to add any of the subcrates to your project. To add the pod5 to do something similar in the example above, run:
cargo add --git https://github.com/bsaintjo/pod5-rs pod5Change pod5 to any of the crates mentioned in the Crates section for other access.
Reading and writing of POD5 files. Currently focused on using polars DataFrame API with further plans to incorporate others.
Exports the Polars POD5 DataFrame API as a Python package. To use this in Python and install in a Python virtual environment, please read the Python installation instructions.
Crate for dealing with non-internal file format details, including file signature and the FlatBuffers footer. Useful for writing and reusing the code with other Arrow handling library or implementations.
Experimental implementation for using reading/writing POD5 files with the official Rust Apache Arrow crate. Maybe useful if you are interested in implementing your own POD5 reader/writer and want to see how to use some of the components in this workspace.
This crate allows for encoding and decoding of nanopore signal data in FAST5/POD5 which are usually compressed in a custom schema.
Licensed under either of
- Apache License, Version 2.0, (LICENSE-APACHE or http://www.apache.org/licenses/LICENSE-2.0)
- MIT license (LICENSE-MIT or http://opensource.org/licenses/MIT)
at your option.
Unless you explicitly state otherwise, any contribution intentionally submitted for inclusion in the work by you, as defined in the Apache-2.0 license, shall be dual licensed as above, without any additional terms or conditions.