Metadata-Version: 2.1
Name: pydbsnp
Version: 0.1.7
Summary: Interface with dbSNP VCF data
Home-page: https://github.com/anthony-aylward/pydbsnp.git
Author: Anthony Aylward
Author-email: aaylward@eng.ucsd.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
Requires-Dist: pysam

# pydbsnp

Interface with dbSNP VCF data

## Installation

First install the python package via `pip3`

```sh
pip3 install pydbsnp
```
or
```sh
pip3 install --user pydbsnp
```

Once the python package is installed, download and index the dbSBP VCF data:

```sh
pydbsnp-download
pydbsnp-index
```

For hg19/GRCh37 coordinates:

```sh
pydbsnp-download --reference-build GRCh37
pydbsnp-index
```

## Command line usage

```sh
pydbsnp-query -h
```

```sh
pydbsnp-query rs689
pydbsnp-query chr11:2160994
pydbsnp-query --reference-build GRCh37 rs689
```

## API

Two classes are provided: `Variant` and `GeneralizedVariant`.

An object of the `Variant` class has an attribute for each relevant field
of the VCF.
```python
from pydbsnp import Variant
v = Variant(id='rs8056814')
print(v.chrom, v.pos, v.id, v.ref, v.alt)
print(v.info)
w = Variant(id='rs8056814', reference_build='GRCh37')
print(w.chrom, w.pos
help(Variant)
```

An object of the `GeneralizedVariant` class is similar, but each attribute
is a tuple which may have multiple items. For example, one RSID may map
to two sets of coordinates.
```python
gv = GeneralizedVariant(id='rs8056814')
print(gv.chrom, gv.pos, gv.id, gv.ref, gv.alt)
```

