<commit_before>[![PyPI](https://img.shields.io/pypi/v/simulatesv.svg)](https://pypi.python.org/pypi/simulatesv/)
[![PyPI](https://img.shields.io/pypi/l/simulatesv.svg)](https://pypi.python.org/pypi/simulatesv/)
[![Build Status](https://travis-ci.org/mlliou112/simulatesv.svg?branch=master)](https://travis-ci.org/mlliou112/simulatesv)

simulatesv
===

Simulate Structural Variations and SNPs for artificial DNA templates. The DNA
templates are generated simply with a pseudo-random number generator, and is
not guided by biological significance. The tool is provided with the intention
of creating a validation set of variants to test current structural variation
detection tools.

## Installation

The recommended method is to install via `pip` or `git clone`. You can also get the
source distribution from [pypi](https://pypi.python.org/pypi/simulatesv/). `pip` will install all the necessary dependencies for you. 
```
$ pip install simulatesv 
```

or

```
$ git clone git@github.com:mlliou112/simulatesv.git
$ python setup.py install
```


## Usage

This script runs with either Python 2 or 3, and requires the Python package `numpy` to run.

If you install via pip, the script will be available to run as `simulatesv.py`, or `python simulatesv.py` if you installed via git clone.

#### Basic

```<commit_msg>updated installation instructions<commit_after>[![PyPI](https://img.shields.io/pypi/v/simulatesv.svg)](https://pypi.python.org/pypi/simulatesv/)
[![PyPI](https://img.shields.io/pypi/l/simulatesv.svg)](https://pypi.python.org/pypi/simulatesv/)
[![Build Status](https://travis-ci.org/mlliou112/simulatesv.svg?branch=master)](https://travis-ci.org/mlliou112/simulatesv)

simulatesv
===

Simulate Structural Variations and SNPs for artificial DNA templates. The DNA
templates are generated simply with a pseudo-random number generator, and is
not guided by biological significance. The tool is provided with the intention
of creating a validation set of variants to test current structural variation
detection tools.

## Installation

The recommended method is to install via `pip` or `git clone`. You can also get the
source distribution from [pypi](https://pypi.python.org/pypi/simulatesv/). `pip` will install all the necessary dependencies for you. 
```
$ pip install simulatesv 
```

or

```
$ git clone <EMAIL>:lioumens/simulatesv.git
$ python setup.py install
```


## Usage

This script runs with either Python 2 or 3, and requires the Python package `numpy` to run.

If you install via pip, the script will be available to run as `simulatesv.py`, or `python simulatesv.py` if you installed via git clone.

#### Basic

```
{'fraction_non_alphanumeric': 0.11742424242424243, 'fraction_numerical': 0.007196969696969697, 'mean_word_length': 4.842920353982301, 'pattern_counts': {'":': 0, '<': 4, '<?xml version=': 0, '>': 4, 'https://': 14, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 1, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '5573529', 'n_tokens_mistral': 857, 'n_tokens_neox': 790, 'n_words': 272}