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fastobo-py Star me

Faultless AST for Open Biomedical Ontologies in Python.

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Overview

fastobo is a Rust library implementing a reliable parser for the OBO file format 1.4. This extension module exports idiomatic Python bindings that can be used to load, edit and serialize ontologies in the OBO format.

Installation

If your platform has no pre-built binaries available, you will need to have the Rust compiler installed. See the documentation on rust-lang.org to learn how to install Rust on your machine.

Installation is then supported through pip:

$ pip install fastobo --user

Usage

An OboDoc instance can be instantiated from a path or from a binary file handle using the fastobo.load function, or from a string using the fastobo.loads function.

import fastobo
obodoc = fastobo.load("../data/ms.obo")

Loading from a gzip file is supported:

import fastobo
import gzip
gzdoc = fastobo.load(gzip.open("../data/cl.obo.gz"))

Feedback

Found a bug ? Have an enhancement request ? Head over to the GitHub issue tracker of the project if you need to report or ask something. If you are filling in on a bug, please include as much information as you can about the issue, and try to recreate the same bug in a simple, easily reproducible situation.

The following people have contributed to this project:

About

This project was developed by Martin Larralde as part of a Master's Degree internship in the BBOP team of the Lawrence Berkeley National Laboratory, under the supervision of Chris Mungall. Cite this project as:

Larralde M. Developing Python and Rust libraries to improve the ontology ecosystem [version 1; not peer reviewed]. F1000Research 2019, 8(ISCB Comm J):1500 (poster) (https://doi.org/10.7490/f1000research.1117405.1)

Metadata

Release files for fastobo 0.14.2

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for fastobo 0.14.2
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fastobo-0.14.2.tar.gz 1.7 MB With provenance Details for fastobo-0.14.2.tar.gz

Built distributions (wheels)

Table of built distributions (wheels) for fastobo 0.14.2
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fastobo-0.14.2-cp314-cp314t-win_amd64.whl CPython 3.14 CPython 3.14 free-threading Windows x86-64 Details for fastobo-0.14.2-cp314-cp314t-win_amd64.whl
fastobo-0.14.2-cp314-cp314t-manylinux_2_28_x86_64.whl CPython 3.14 CPython 3.14 free-threading Linux glibc 2.28+ x86-64 Details for fastobo-0.14.2-cp314-cp314t-manylinux_2_28_x86_64.whl
fastobo-0.14.2-cp314-cp314t-manylinux_2_28_aarch64.whl CPython 3.14 CPython 3.14 free-threading Linux glibc 2.28+ ARM64 Details for fastobo-0.14.2-cp314-cp314t-manylinux_2_28_aarch64.whl
fastobo-0.14.2-cp314-cp314t-macosx_12_0_x86_64.whl CPython 3.14 CPython 3.14 free-threading macOS 12.0+ x86-64 Details for fastobo-0.14.2-cp314-cp314t-macosx_12_0_x86_64.whl
fastobo-0.14.2-cp314-cp314t-macosx_11_0_arm64.whl CPython 3.14 CPython 3.14 free-threading macOS 11.0+ ARM64 Details for fastobo-0.14.2-cp314-cp314t-macosx_11_0_arm64.whl
fastobo-0.14.2-cp312-abi3-win_amd64.whl CPython 3.12 abi3 Windows x86-64 Details for fastobo-0.14.2-cp312-abi3-win_amd64.whl
fastobo-0.14.2-cp312-abi3-manylinux_2_28_x86_64.whl CPython 3.12 abi3 Linux glibc 2.28+ x86-64 Details for fastobo-0.14.2-cp312-abi3-manylinux_2_28_x86_64.whl
fastobo-0.14.2-cp312-abi3-manylinux_2_28_aarch64.whl CPython 3.12 abi3 Linux glibc 2.28+ ARM64 Details for fastobo-0.14.2-cp312-abi3-manylinux_2_28_aarch64.whl
fastobo-0.14.2-cp312-abi3-macosx_12_0_x86_64.whl CPython 3.12 abi3 macOS 12.0+ x86-64 Details for fastobo-0.14.2-cp312-abi3-macosx_12_0_x86_64.whl
fastobo-0.14.2-cp312-abi3-macosx_11_0_arm64.whl CPython 3.12 abi3 macOS 11.0+ ARM64 Details for fastobo-0.14.2-cp312-abi3-macosx_11_0_arm64.whl
fastobo-0.14.2-cp311-cp311-win_amd64.whl CPython 3.11 CPython 3.11 Windows x86-64 Details for fastobo-0.14.2-cp311-cp311-win_amd64.whl
fastobo-0.14.2-cp311-cp311-manylinux_2_28_x86_64.whl CPython 3.11 CPython 3.11 Linux glibc 2.28+ x86-64 Details for fastobo-0.14.2-cp311-cp311-manylinux_2_28_x86_64.whl
fastobo-0.14.2-cp311-cp311-manylinux_2_28_aarch64.whl CPython 3.11 CPython 3.11 Linux glibc 2.28+ ARM64 Details for fastobo-0.14.2-cp311-cp311-manylinux_2_28_aarch64.whl
fastobo-0.14.2-cp311-cp311-macosx_12_0_x86_64.whl CPython 3.11 CPython 3.11 macOS 12.0+ x86-64 Details for fastobo-0.14.2-cp311-cp311-macosx_12_0_x86_64.whl
fastobo-0.14.2-cp311-cp311-macosx_11_0_arm64.whl CPython 3.11 CPython 3.11 macOS 11.0+ ARM64 Details for fastobo-0.14.2-cp311-cp311-macosx_11_0_arm64.whl
fastobo-0.14.2-cp310-cp310-win_amd64.whl CPython 3.10 CPython 3.10 Windows x86-64 Details for fastobo-0.14.2-cp310-cp310-win_amd64.whl
fastobo-0.14.2-cp310-cp310-manylinux_2_28_x86_64.whl CPython 3.10 CPython 3.10 Linux glibc 2.28+ x86-64 Details for fastobo-0.14.2-cp310-cp310-manylinux_2_28_x86_64.whl
fastobo-0.14.2-cp310-cp310-manylinux_2_28_aarch64.whl CPython 3.10 CPython 3.10 Linux glibc 2.28+ ARM64 Details for fastobo-0.14.2-cp310-cp310-manylinux_2_28_aarch64.whl
fastobo-0.14.2-cp310-cp310-macosx_12_0_x86_64.whl CPython 3.10 CPython 3.10 macOS 12.0+ x86-64 Details for fastobo-0.14.2-cp310-cp310-macosx_12_0_x86_64.whl
fastobo-0.14.2-cp310-cp310-macosx_11_0_arm64.whl CPython 3.10 CPython 3.10 macOS 11.0+ ARM64 Details for fastobo-0.14.2-cp310-cp310-macosx_11_0_arm64.whl
fastobo-0.14.2-cp39-cp39-win_amd64.whl CPython 3.9 CPython 3.9 Windows x86-64 Details for fastobo-0.14.2-cp39-cp39-win_amd64.whl
fastobo-0.14.2-cp39-cp39-manylinux_2_28_x86_64.whl CPython 3.9 CPython 3.9 Linux glibc 2.28+ x86-64 Details for fastobo-0.14.2-cp39-cp39-manylinux_2_28_x86_64.whl
fastobo-0.14.2-cp39-cp39-manylinux_2_28_aarch64.whl CPython 3.9 CPython 3.9 Linux glibc 2.28+ ARM64 Details for fastobo-0.14.2-cp39-cp39-manylinux_2_28_aarch64.whl
fastobo-0.14.2-cp39-cp39-macosx_12_0_x86_64.whl CPython 3.9 CPython 3.9 macOS 12.0+ x86-64 Details for fastobo-0.14.2-cp39-cp39-macosx_12_0_x86_64.whl
fastobo-0.14.2-cp39-cp39-macosx_11_0_arm64.whl CPython 3.9 CPython 3.9 macOS 11.0+ ARM64 Details for fastobo-0.14.2-cp39-cp39-macosx_11_0_arm64.whl

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