NGLessPy 0.2

NGLessPy: Python interface to NGLess

# NGLessPy: NGLess as a Python Embedded Language

This is a variation of [NGLess](http://ngless.embl.de) as an embedded language
in Python, thus enabling processing of next generation data through a Python
API. See the example below.

[](https://travis-ci.org/luispedro/nglesspy)
[](https://raw.githubusercontent.com/hyperium/hyper/master/LICENSE)
[](https://gitter.im/luispedro/ngless?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)

This is **very experimental** and can change at any time. Please [get in
touch](mailto:[e-mail]) if you want to use it in your work. For
questions, you can also use the [ngless mailing
list](https://groups.google.com/forum/#!forum/ngless).

## Dependencies

- [requests](http://docs.python-requests.org/)
- [NGLess](http://ngless.embl.de)

NGLesspy can auto-install ngless if it needs to.

NGLesspy is compatible with Python 2.7 and 3.4+.

## Example


Inside the [bin/](https://github.com/luispedro/nglesspy/tree/master/bin)
directory, you will find several simple scripts exposing NGLess functionality
as command line tools. These are also simple examples of how NGLessPy can be
used.

See the [tutorial](http://ngless.embl.de/nglesspy.html) for a more thorough
explanation of what is going on in the example below.

```python
from ngless import NGLess

sc = NGLess.NGLess('0.8')

sc.import_('mocat', '0.0')
e = sc.env

e.sample = sc.load_mocat_sample_('testing')

@sc.preprocess_(e.sample, using='r')
def proc(bk):
bk.r = sc.substrim_(bk.r, min_quality=25)

e.mapped = sc.map_(e.sample, reference='hg19')
e.mapped = sc.select_(e.mapped, keep_if=['{mapped}'])

sc.write_(e.mapped, ofile='ofile.sam')

sc.run()
```

This is equivalent to the NGLess script


ngless '0.8'
import 'mocat' version '0.0'

sample = load_mocat_sample('testing')

preprocess_(sample) using='r':
r = substrim(r, min_quality=25)

mapped = map(sample, reference='hg19')
mapped = select(mapped, keep_if=[{mapped}])

write(mapped, ofile='ofile.sam')