pybwtool 1.0.8

Extract

The extract method returns a tuple of pandas Dataframes with the data from the regions of a bed file extracted from the given bigwig.

from pybwtool import extract

results = extract(
    bed_path="path/to/my/bed_file.bed",
    bigwig_path="path/to/my/bigwig_file.bigwig"
)

You can also run the extraction directly to a file, a thing that can get handy when you have to run a very big bed file. You just need to specify a target file.

from pybwtool import extract

extract(
    bed_path="path/to/my/bed_file.bed",
    bigwig_path="path/to/my/bigwig_file.bigwig",
    target="target.bed"
)

It is also possible to directly export to a compressed file just by adding the gzip extension, as follows:

from pybwtool import extract

extract(
    bed_path="path/to/my/bed_file.bed",
    bigwig_path="path/to/my/bigwig_file.bigwig",
    target="target.bed.gz"
)