RT Journal Article
SR Electronic
T1 BioCantor: a Python library for genomic feature arithmetic in arbitrarily related coordinate systems
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.07.09.451743
DO 10.1101/2021.07.09.451743
A1 Pamela H. Russell
A1 Ian T. Fiddes
YR 2021
UL http://biorxiv.org/content/early/2021/07/10/2021.07.09.451743.abstract
AB Motivation Bioinformaticians frequently navigate among a diverse set of coordinate systems: for example, converting between genomic, transcript, and protein coordinates. The abstraction of coordinate systems and feature arithmetic allows genomic workflows to be expressed more elegantly and succinctly. However, no publicly available software library offers fully featured interoperable support for multiple coordinate systems. As such, bioinformatics programmers must either implement custom solutions, or make do with existing utilities, which may lack the full functionality they require.Results We present BioCantor, a Python library that provides integrated library support for arbitrarily related coordinate systems and rich operations on genomic features, with I/O support for a variety of file formats.Availability and implementation BioCantor is implemented as a Python 3 library with a minimal set of external dependencies. The library is freely available under the MIT license at https://github.com/InscriptaLabs/BioCantor and on the Python Package Index at https://pypi.org/project/BioCantor/. BioCantor has extensive documentation and vignettes available on ReadTheDocs at https://biocantor.readthedocs.io/en/latest/.Competing Interest StatementThe authors have declared no competing interest.