Metadata-Version: 2.4
Name: dask-pgen
Version: 0.1.2
Summary: Dask interface for memory-efficient reading PLINK genotype files
Home-page: https://github.com/kangchenghou/dask-pgen
Author: Kangcheng Hou
Author-email: kangchenghou@gmail.com
Description-Content-Type: text/markdown
Requires-Dist: dask
Requires-Dist: pandas
Requires-Dist: numpy
Requires-Dist: natsort
Requires-Dist: fire
Requires-Dist: structlog
Requires-Dist: Pgenlib
Dynamic: author
Dynamic: author-email
Dynamic: description
Dynamic: description-content-type
Dynamic: home-page
Dynamic: requires-dist
Dynamic: summary

# dask-pgen
Lazy loading PLINK genotype data (.pgen or .bed) file with dask array.

# Installation

```bash
pip install dask-pgen
```

or, 
```bash
pip install -U cython numpy
git clone https://github.com/KangchengHou/dask-pgen.git
cd dask-pgen; pip install -e .
```

# Example
```bash
# if dapgen is not found, set the path of dapgen yourself
# chmod +x dask-pgen/bin/dapgen
# dapgen=dask-pgen/bin/dapgen
# replace "dapgen" with "$dapgen"

dapgen score \
    --plink <plink> \
    --weights <weights_path> \
    --weight-col-prefix <weight_column_prefix> \
    --chrom-col CHR --pos-col POS --alt-col A1 --ref-col A2 \
    --out <out_path> \
    --center True # center the genotype or not, default is False \
    --threads 4 \
    --memory 20000
```
