<commit_before># veppy (alpha)

**WARNING: This code is an alpha release and not production-ready. APIs may change at any time.**

A genetic variant effect predictor for Python. Inspired by SnpEff and VEP.


## Installation

```
python setup.py install
```

## Setup

### Prepare a directory for veppy data

The default data path is: `./data`

(OPTIONAL) You can override this by setting `$VEPPY_DATA_DIR`.

```
export VEPPY_DATA_DIR=/opt/veppy
```

### Download source data and build indexes

**NOTE: This step downloads about 1gb of data. After indexing, the data directory will consume about 8gb of disk space.**

```
./scripts/download_data_GRCh37.sh
```

### Build indexes (this only needs to be done once)

```
python ./run_index.py
```

## Example Usage

```
from veppy.veppy import calculate_consequences
variant = ('1', 8025384, 'A', 'T')
result = calculate_consequences('GRCh37', *variant)
print result.results
```


## Testing

Tests are based on chr1 versions of input data (TODO upload this somewhere)

```
$ nosetests
```

Coverage:
```
$ nosetests --with-coverage --cover-package=veppy
```


## About SolveBio

SolveBio is a genomics company based in New York City.

[[https://s3.amazonaws.com/veppy/solvebio_logo.png|alt=SolveBio](https://www.solvebio.com/)]
<commit_msg>try to fix url<commit_after># veppy (alpha)

**WARNING: This code is an alpha release and not production-ready. APIs may change at any time.**

A genetic variant effect predictor for Python. Inspired by SnpEff and VEP.


## Installation

```
python setup.py install
```

## Setup

### Prepare a directory for veppy data

The default data path is: `./data`

(OPTIONAL) You can override this by setting `$VEPPY_DATA_DIR`.

```
export VEPPY_DATA_DIR=/opt/veppy
```

### Download source data and build indexes

**NOTE: This step downloads about 1gb of data. After indexing, the data directory will consume about 8gb of disk space.**

```
./scripts/download_data_GRCh37.sh
```

### Build indexes (this only needs to be done once)

```
python ./run_index.py
```

## Example Usage

```
from veppy.veppy import calculate_consequences
variant = ('1', 8025384, 'A', 'T')
result = calculate_consequences('GRCh37', *variant)
print result.results
```


## Testing

Tests are based on chr1 versions of input data (TODO upload this somewhere)

```
$ nosetests
```

Coverage:
```
$ nosetests --with-coverage --cover-package=veppy
```


## About SolveBio

SolveBio is a genomics company based in New York City.

[![SolveBio](https://s3.amazonaws.com/veppy/solvebio_logo.png|alt=SolveBio)](https://www.solvebio.com/)

{'fraction_non_alphanumeric': 0.12877030162412992, 'fraction_numerical': 0.01237432327919567, 'mean_word_length': 4.412133891213389, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 4, 'lorem ipsum': 0, 'www.': 2, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 6, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6377860', 'n_tokens_mistral': 924, 'n_tokens_neox': 818, 'n_words': 291}