# NGLessPy: NGLess in Python

Note As of Oct 2017, NGLess is considered beta software (we believe it works, but there may still be a few rough edges), while NGLessPy is alpha software (very experimental).

## Install

```bash

pip install NGLessPy

```

(or from source, using the standard python setup.py install)

## Basic Tutorial

This tutorial expects a certain familiarity with general ngless concepts and functions.

We start by importing the NGLess object:

```python

from ngless import NGLess

```

We now build an NGLess.NGLess object, giving it the version of ngless we wish (this is like the version declaration at the top of an NGLess file:

```python

sc = NGLess.NGLess(‘0.8’)

```

To simplify the rest of the script, we are going to use the short name e to refer to the environment of the script we are generating. The environment is what will hold the ngless variables we will use:

```python

e = sc.env

```

We can import ngless modules using the import_ function (using name and version):

```python

sc.import_(‘mocat’, ‘0.0’)

```

Now, we can use all NGLesss functionality. Functions get an underscore at the end, like this:

```python

e.sample = sc.load_mocat_sample_(‘testing’)

```

preprocess_ is special because it takes a block in ngless, which maps to it taking a function in Python. We can use decorator syntax to do it all compactly:

```python

@sc.preprocess_(e.sample, using=’r’) def proc(bk):

# bk is the block environment, where r is defined bk.r = sc.substrim_(bk.r, min_quality=25)

```

Now, we map against hg19 and filter it. As you can see, ngless functions are called with an extra underscore and variables are kept in the e object:

```python

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

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

```

Finally, we execute the resulting script:

```python

sc.run(auto_install=True)

```

This will even install NGLess if it is not available in the PATH.

## Full script

```python

from ngless import NGLess

sc = NGLess.NGLess(‘0.8’) e = sc.env

sc.import_(‘mocat’, ‘0.0’)

e.sample = sc.load_mocat_sample_(‘testing’) @sc.preprocess_(e.sample, using=’r’) def proc(bk):

# bk is the block environment, where r is defined 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(auto_install=True)

```