NGLessPy: Python interface to NGLess
Project description
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.
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')
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