Metadata-Version: 2.1
Name: py1kgp
Version: 0.1.2
Summary: Utilities for working with 1000 Genomes data
Home-page: https://gitlab.com/aaylward/py1kgp
Author: Anthony Aylward
Author-email: aaylward@salk.edu
License: UNKNOWN
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
License-File: LICENSE

# py1kgp

Utilities for working with 1000 Genomes data

## Installation

First make sure you have followed the installation procedure for
[pydbsnp](https://github.com/anthony-aylward/pydbsnp). Then install `py1kgp`
with `pip3`:

```sh
pip3 install py1kgp
```
or
```sh
pip3 install --user py1kgp
```

For full functionality, you should appropriately set the environment variable
`PY1KGP_DIR`. For example, you could add this to your `.bash_profile`:

```bash
export PY1KGP_DIR=<path to directory of your choice>
```

## Examples

```python
import py1kgp
py1kgp.Variant('rs10')
py1kgp.Variant(id='rs10')
py1kgp.Variant(7, 92383888)
py1kgp.Variant(chrom=7, pos=92383888)
py1kgp.fast_genotypes(7, 92383888)
py1kgp.fast_genotypes(7, 92383888, samples='NA21142,NA21143,NA21144')
py1kgp.fast_maf(7, 92383888)
py1kgp.slice_vcf(1, 1000000, 2000000)
py1kgp.slice_vcf(1, 1000000, 2000000, samples='NA21142,NA21143,NA21144')
py1kgp.slice_vcf(1, 1000000, 2000000, samples='AFR')
py1kgp.slice_vcf(1, 1000000, 2000000, samples='samples.panel')
```

