The package providies utilties to parse and query commonly used genomic file formats. Genomic files are usually indexed (BigWig, BigBed, Tabix etc) and the library will only read the necessary bytes of the file to query data. In addition, The library also works with remotely hosted files. This requires the remotely hosted file to support HTTP Byte-Range requests


  • package is open source and is available on GitHub


Using PyPI

will be on PyPI soon.. but for now install from GitHub below

From GitHub (devel version)

To install the devel version from GitHub: Install using pip

pip install

or clone the repository and install from local directory using pip


Depending on how python was setup, installing packages may sometime require sudo permission, in this case, add the –user option

pip install --user


For example, to read a BigWig file,

from epivizFileParser import BigWig

# initialize a file
bw = BigWig("tests/")

# extract header and zoom levels from the file
print(bw.header, bw.zooms)

# query the file
res, err = bw.getRange(chr="chr1", start=10000000, end=10020000)

# summarize data into equals windows/bins
sres = bw.bin_rows(res, chr="chr1", start=10000000, end=10020000, columns=['score'], bins=10)


Indices and tables