Metadata-Version: 2.4
Name: wheely-radiant
Version: 1.1.1
Summary: Reader for Radiant DIA results, compatible with wheely-mammoth
Home-page: https://github.com/seerbio/wheely-radiant
Author: Seth Just
Author-email: sjust@seer.bio
Project-URL: Bug Tracker, https://github.com/seerbio/wheely-radiant/issues
Classifier: Programming Language :: Python :: 3
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE.md
Requires-Dist: pyspark[sql]<4.0.0,>=3.5.0
Requires-Dist: wheely-mammoth<1.0.0,>=0.16.3
Requires-Dist: importlib_metadata; python_version < "3.8"
Provides-Extra: docs
Requires-Dist: numpydoc>=1.0.0; extra == "docs"
Requires-Dist: sphinx-argparse>=0.2.5; extra == "docs"
Requires-Dist: sphinx-rtd-theme>=0.5.0; extra == "docs"
Requires-Dist: nbsphinx>=0.7.1; extra == "docs"
Requires-Dist: ipykernel>=5.3.0; extra == "docs"
Requires-Dist: recommonmark>=0.5.0; extra == "docs"
Provides-Extra: dev
Requires-Dist: pre-commit>=2.7.1; extra == "dev"
Requires-Dist: black>=20.8b1; extra == "dev"
Requires-Dist: pytest; extra == "dev"
Requires-Dist: pandas; extra == "dev"
Dynamic: license-file

**wheely-radiant**: Reader for Radiant DIA results, compatible with
[`wheely-mammoth`](https://github.com/seerbio/wheely-mammoth).

## Installation  

This library requires Python 3.8+ and can be installed with pip:  

```shell
pip install wheely-radiant
```

## Basic Usage

This package provides a plugin for the [Fulcrum Pipeline](https://github.com/seerbio/fulcrum/)'s
`read_existing` search backend.

After installing `wheely-radiant` you may use the `radiant` engine to load
existing Radiant DIA results:

```toml
[search]
backend = "read_existing"
engine = "radiant"
location = ["uri_one", "uri_two", ...]
```

(or similar in JSON or `dict` format)

## Direct Usage

To load raw PSM scores from a Radiant Parquet (`.radiantDIA`) file, use the function
`read_radiant_features()`.

```pycon
>>> from wheely_radiant import read_radiant_features
>>> ds = read_radiant_features("data/1.mzML.subset.radiantDIA")
>>> type(ds)
<class 'wheely.mammoth.dataset.PsmDataset'>
>>> ds.scores.select(ds.score_columns[1]).describe().toPandas()
  summary            cosineSim
0   count                 1000
1    mean   0.3947062000000001
2  stddev  0.15665395271892263
3     min               0.0315
4     max               0.9926
```

To read multiple files, pass a tuple, list, array, or series of file paths.
Currently only full paths are supported; you can not pass wildcard ("glob")
paths to the function.
