https://github.com/ngless-toolkit/nglesspy

NGLess as a Python embedded language (experimental)
https://github.com/ngless-toolkit/nglesspy

domain-specific-language embedded-language experimental genomics metagenomics next-generation-sequencing ngless python python-embedded-language

Last synced: 6 months ago
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NGLess as a Python embedded language (experimental)

• Host: GitHub
• URL: https://github.com/ngless-toolkit/nglesspy
• Owner: ngless-toolkit
• Created: 2017-08-29T15:39:11.000Z (about 8 years ago)
• Default Branch: master
• Last Pushed: 2020-07-16T19:57:43.000Z (about 5 years ago)
• Last Synced: 2025-03-22T08:18:09.583Z (7 months ago)
• Topics: domain-specific-language, embedded-language, experimental, genomics, metagenomics, next-generation-sequencing, ngless, python, python-embedded-language
• Language: Python
• Homepage: http://ngless.embl.de
• Size: 48.8 KB
• Stars: 2
• Watchers: 1
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Changelog: ChangeLog

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README

          
# 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.

[![Build Status](https://travis-ci.org/ngless-toolkit/nglesspy.svg?branch=master)](https://travis-ci.org/ngless-toolkit/nglesspy)

[![MIT licensed](https://img.shields.io/badge/license-MIT-blue.svg)](https://raw.githubusercontent.com/hyperium/hyper/master/LICENSE)

This is **very experimental** and can change at any time. Please [get in

touch](mailto:coelho@embl.de) 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')

    sample = 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')