prstools 0.0.58
Convenient and powerfull Polygenic Risk Score creation.
License: MIT License
Requires Python: >=3.8
Keywords: PRS PGS polygenic genomics prediction genetics

# prstools


<!-- WARNING: THIS FILE WAS AUTOGENERATED! DO NOT EDIT! -->

`prstools` is software to create Polygenic Risk Scores (PRS) directly
from the commandline <br> (and optionally from inside python).

It makes PRS generation easier, compared to previous tools, by:

- Super fast reading and matching of sumstats (handles odd formats)
- Rapid creation of the model (about 20x faster than earlier PRS-CS)
- Automatic generation of the PRS Prediction for target plink files.

All the above, for a real GWAS sumstat, within 30 minutes using only
**1** command .

Installation and running the demo example should not take more than 10
minutes.

We are actively developing `prstools` and feedback by mail or our
[feedback form](https://forms.gle/TnvNyBX6qDy7Vupn9) (with 🏆 lottery)
is much appreciated!

## Install

To install use the following command.

``` sh
pip install -U prstools
```

For it to work, you should have python3.8 or later installed (`pip` is
included in python3.8+). If the command above does not work directly you
can install installed using `conda` (or `mamba` if you have that), by
running `conda install "python>=3.9"` For other install issues please
check the (install guide is still pretty basic) [install
guide](https://github.com/mennojw/prstools-release/blob/main/tutorials/00_install_guide.ipynb)
or send us a mail.

## How to use

Next to this very brief discription of what `prstools` can do, there is
also more complete [Getting Started
Tutorial](https://github.com/mennojw/prstools-release/blob/main/tutorials/01_getting_started.ipynb).
Immediately after installing `prstools`, it should be possible to
download & run the demo example (~4mb), by pasting the following into
the commandline (if not see
[guide](https://github.com/mennojw/prstools-release/blob/main/tutorials/00_install_guide.ipynb)):

``` bash
# Makes 'example' dir with data in current path:
prstools downloadutil --pattern example --destdir ./; cd example

# Run the model with example data:
prstools prscs2 --ref ldref_1kg_pop --target target \
                --sst sumstats.tsv --n_gwas 2565 --out --pred ./result 
```

This will run PRS-CS2 on the example data, using the new implementation
to demonstrate the capabilities of `prstools` and makes PRS predictions
for the example dataset.

<br> More generally you can use `prstools` by typing into the
command-line interface:

``` bash
prstools
```

``` console
Usage:
 prstools <command> ...

Convenient and powerfull Polygenic Risk Score creation. 
'prst' is a commandline shorthand for 'prstools'

Models & Utility Commands:
 <command>
  downloadutil  Download and unpack LD reference panels and other data.
  combine       A tool to combine genetics-related text files.
  prscs2        PRS-CS v2: A polygenic prediction method that infers posterior SNP effect sizes
                under continuous shrinkage (CS) priors.
```

<br> By combining `prstools` with another `<command>` a specific model
or other functionality can be used. <br> Forinstance typing
`prstools prscs2` will output a help for the prscs2 subcommand:

``` console
Usage:
 prstools prscs2 [-h  --cpus <number-of-cpus>] --ref <dir/refcode> --target <bim-prefix>
                       --sst <file> --out <dir+prefix> [--n_gwas <num>  --chrom <chroms>]
                       [--colmap <alternative_colnames>  --pred  --n_iter <n_iter>]
                       [--n_burnin <n_burnin>  --n_slice <n_slice>  --seed <seed>  --a <a>]
                       [--b <b>  --phi <phi>  --clip <clip>  --sampler <sampler>]

PRS-CS v2: A polygenic prediction method that infers posterior SNP effect sizes under continuous shrinkage (CS) priors.

General Options:
 -h, --help                               Show this help message and exit.
 -c, --cpus <number-of-cpus>              The number of cpus to use. Generally most efficient if
                                          chosen to be between 1 and 5. Functionality can be

... [omitted for readability] ...


 --clip <clip>                            Clip parameter. The default works best in pretty much
                                          all cases. (default: 1.0)
 --sampler <sampler>                      Sampler algorithm. Rue sampling is the original sampler,
                                          which gives good results. (default: Rue)

Examples --> can be directly copy-pasted (:
 prst downloadutil --pattern example --destdir ./; cd example                                                # Makes 'example' dir in current path.
 prstools prscs2 --ref ldref_1kg_pop --target target --sst sumstats.tsv --n_gwas 2565 --out ./result-prscs2 # Run the model with example data.
 prst prscs2 -r ldref_1kg_pop -t target -s sumstats.tsv -n 2565 -o ./result-prscs2 --pred                  # A shorter version of previous that also does the predictions.
```

As can be seen, there are examples at the end of the help output to
illustrate usage, which should work with a simple copy-paste. <br> <br>

## Tutorial

For more information and a hands on demonstration of what `prstools` can
do have a look at the [Getting Started
Tutorial](https://github.com/mennojw/prstools-release/blob/main/tutorials/01_getting_started.ipynb).
There is also a [video version of this
tutorial](https://youtu.be/BP1zUBFH2l8). You can load the tutorial in a
free cloud instance by clicking here: [![Google
Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/mennojw/prstools-release/blob/main/tutorials/01_getting_started.ipynb).

## Contact

For questions and support please send a mail
(menno.j.witteveen@gmail.com).