fibertools-rs 0.3.2

Fiber-seq toolkit in rust
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---
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# `fibertools-rs`

<img src="./assets/img/fiber_tools_teal.png#gh-dark-mode-only" alt="fibertools-rs dark logo" width="200"/>
<img src="./assets/img/fiber_tools_grey.png#gh-light-mode-only" alt="fibertools-rs light logo" width="200"/>

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`fibertools-rs` a CLI tool for creating and interacting with fiberseq bam files.

# Install [![Conda (channel only)](https://img.shields.io/conda/vn/bioconda/fibertools-rs?color=green)](https://anaconda.org/bioconda/fibertools-rs)

`fibertools-rs` is avalible through `bioconda` and can be installed with the following command:

```bash
mamba install -c conda-forge -c bioconda fibertools-rs
```

However, the `bioconda` version currently does not support GPU acceleration. If you would like to use GPU acceleration, you will need to install using the directions in the [INSTALL.md](/INSTALL.md) file.

# Usage

```bash
ft --help
```

[Help page for fibertools](/docs/ft--help.md)

# Subcommands for `fibertools-rs`

## `ft predict-m6a`

Predict m6A positions using HiFi kinetics data and encode the results in the MM and ML bam tags. [Help page for predict-m6a](/docs/ft-predict-m6a-help.md).

## `ft add-nucleosomes`

Add nucleosomes to a bam that file already contains m6a predictions. Note, this process is also run in the background during `predict-m6a`, so it is unnecessary to run independently unless you want to try new parameters for nucleosome calling. [Help page for add-nucleosomes](/docs/ft-add-nucleosomes-help.md).

## `ft extract`

Extracts fiberseq data from a bam file into plain text. [Help page for extract](/docs/ft-extract-help.md).

### `ft extract --all`

The extract all option is a special option that tries to extract all the fiberseq data into a tabular format. The following is an image of the output. Note that the [column names](/docs/ft-all-columns.md) will be preserved across different software versions (unless otherwise noted); however, the order may change and new columns may be added. Therefore, when loading the data (with `pandas` e.g.) be sure to use the column names as opposed to indexes for manipulation.
![ft-extract all](/assets/img/ft-extract-all.png)

## `ft center`

Center fiberseq reads (bam) around reference position(s). [Help page for center](/docs/ft-center-help.md).
![Center](/assets/img/center.png)

# Python API (`pyft`)

The python API is still in development and not stable; however, you can find the current code progress in the [py-ft](/py-ft) folder. More information available at [readthedocs](https://py-ft.readthedocs.io/en/latest/).

# Cite

**Jha, A.**, **Bohaczuk, S. C.**, Mao, Y., Ranchalis, J., Mallory, B. J., Min, A. T., Hamm, M. O., Swanson, E., Finkbeiner, C., Li, T., Whittington, D., Stergachis, A. B., & **Vollger, M. R.** (2023). Fibertools: fast and accurate DNA-m6A calling using single-molecule long-read sequencing. _bioRxiv_. https://doi.org/10.1101/2023.04.20.537673

# Read the fibertools library docs

You can find the docs for the latest release here:
[https://docs.rs/fibertools-rs/latest/fibertools_rs/](https://docs.rs/fibertools-rs/latest/fibertools_rs/)
or download from source and run:

```
cargo doc --open
```

and the docs will open in your browser.

# TODO items

- [ ] Use new iterator for `ft extract` and group writes to try and improve the speed
- [ ] long format extract command
- [ ] Improve progress bar for predict-m6a.
  - [ ] Get size of bam, say how far we are through the bam in terms of MB/GB?
- [x] Add a python API (see py-ft for progress)
  - [x] extract api
  - [x] center api
  - [ ] improve docs
  - [ ] add default data viz
  - [ ] add conversion to pandas data frame or maybe anndata
- [x] GPU support
  - [ ] see if I can simplify or statically link PyTorch to get it onto bioconda
  - [ ] Detect GPU memory to set batch size dynamically.
- [ ] Add unaligned, secondary, supplemental reads to the test bam.
- [x] add option result to bamlift
- [x] improve speed of liftover closest in bamlift. It takes about 50% of the time.
- [x] Add more test cases, learn about test modules in folders
- [x] Set filters for ML depending on the model used

# Contributing

If you would like to contribute to `fibertools-rs`, please see the [CONTRIBUTING.md](/CONTRIBUTING.md) file for more information.