Skip to main content

Python wrapper for the bwtool library.

Project description

Travis CI build SonarCloud Quality SonarCloud Maintainability Codacy Maintainability Maintainability Pypi project Pypi total project downloads

Python wrapper for the bwtool library. Please take a look to the bwtool wiki for notes on the installation process and to the known issues listed below within this readme.

How do I install this package?

As usual, just download it using pip:

pip install pybwtool

Tests Coverage

Since some software handling coverages sometimes get slightly different results, here’s three of them:

Coveralls Coverage SonarCloud Coverage Code Climate Coverate

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"
)

Common fixes for getting bwtool to work

Consider looking at the Travis-CI configuration. If it works there, it should also work for you.

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for pybwtool, version 1.0.8
Filename, size File type Python version Upload date Hashes
Filename, size pybwtool-1.0.8.tar.gz (4.9 kB) File type Source Python version None Upload date Hashes View

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring DigiCert DigiCert EV certificate Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page