NGLess as a Python embedded language (experimental)
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README.md

NGLessPy: NGLess as a Python Embedded Language

This is a variation of NGLess as an embedded language in Python, thus enabling processing of next generation data through a Python API. See the example below.

Build Status MIT licensed Join the chat at https://gitter.im/luispedro/ngless

This is very experimental and can change at any time. Please get in touch if you want to use it in your work. For questions, you can also use the ngless mailing list.

Dependencies

NGLesspy can auto-install ngless if it needs to.

NGLesspy is compatible with Python 2.7 and 3.4+.

Example

Inside the 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 for a more thorough explanation of what is going on in the example below.

    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')