Metadata-Version: 2.1
Name: LDtoolsets
Version: 0.0.10
Summary: Modules for LD computing, liftover and region extraction
Home-page: https://github.com/changebio/LDtools/tree/master/
Author: YinHuang
Author-email: changebio@yeah.net
License: Apache Software License 2.0
Keywords: LD computing,Liftover,Region extraction
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: License :: OSI Approved :: Apache Software License
Requires-Python: >=3.6
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: pip
Requires-Dist: packaging
Requires-Dist: torch
Requires-Dist: numpy
Requires-Dist: pandas
Requires-Dist: scipy
Requires-Dist: dask
Requires-Dist: bgen-reader
Requires-Dist: pandas-plink (==2.2.5)
Requires-Dist: liftover
Requires-Dist: Biopython
Requires-Dist: pybgen
Provides-Extra: dev

# Scalable pipeline for computing LD matrix in big sample phenotype



### 4 modules
- Genodata
- Sumstats
- Liftover
- LDmatrix

## Install

`pip install LDtoolsets`

## How to use

```python
lf = Liftover('hg38','hg19')
```

```python
vcf ='/home/yh3455/Github/SEQLinkage/MWE/small_sample_ii_coding.vcf.gz'
```

```python
lf.vcf_liftover(vcf)
```

```python
!which python
```

    /home/yh3455/miniconda3/bin/python



