Metadata-Version: 2.1
Name: cs2star
Version: 0.4.1
Summary: A simple utility to convert cryosparc particle positions to relion star format.
Home-page: https://github.com/brisvag/cs2star/
Author: Lorenzo Gaifas
Author-email: brisvag@gmail.com
License: GNU General Public License v3 (GPLv3)
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Programming Language :: Python
Requires-Python: >=3.7
Description-Content-Type: text/markdown
License-File: LICENSE

# cs2star

A simple utility that wraps around `csparc2star.py` to convert particle positions from Cryosparc JOB directories into a RELION-ready directory. On top of what `csparc2star.py` already does, this script automatically symlinks (or copies) the `.mrc` files, renaming them as appropriate to `mrcs` and updating the `rlnMicrographName` column to reflect the change.

# Installation

This package requires [pyem](https://github.com/asarnow/pyem), which is not available on pip under that name (there is a pyem on pip; that's a different package!). To install it manually:

```bash
git clone https://github.com/asarnow/pyem.git
cd pyem
pip install -e .
```

You can then install `cs2star` with pip:

```bash
pip install cs2star
```

# Usage

```bash
cs2star cryosparc_job_dir [dest_dir]
```

A couple more options are available, check out the help page with `-h`.

## Example

Assuming `Cryosparc/J23` is a classification job:

```bash
cs2star Cryosparc/J23 -p
```

will create in the working directory:
- a relion-ready `particles.star`
- a `patches` directory containing the particle images to be used by relion refinement
You can now run `relion` and provide `particles.star` as the input.

## Tips

- While you can use the `--class` option to select specific classes from a cryosparc job, the class indexes do not correspond the the class order in Cryosparc (which is simply based on particle number). A much easier way to select specific classes to convert to `.star` is to use the `select 2D classes` job in cryosparc, then provide this job as input to cs2star.
- `--swapxy` defaults to `True`. This is because *usually* that's what you need; unfortunately, this may differ on a case by case basis, so make sure to check the data after conversion with you favourite viewer to ensure that particles are correctly centered.
