# `fastobo-py` [](https://github.com/fastobo/fastobo-py/stargazers)
*Faultless AST for Open Biomedical Ontologies in Python.*
[](https://github.com/fastobo/fastobo-py/actions)
[](https://codecov.io/gh/fastobo/fastobo-py)
[](https://choosealicense.com/licenses/mit/)
[](https://github.com/fastobo/fastobo-py/)
[](https://pypi.org/project/fastobo)
[](https://pypi.org/project/fastobo/#files)
[](https://anaconda.org/bioconda/fastobo)
[](https://pypi.org/project/fastobo/#files)
[](https://pypi.org/project/fastobo/#files)
[](https://github.com/fastobo/fastobo-py/blob/master/CHANGELOG.md)
[](https://fastobo.readthedocs.io/)
[](https://github.com/fastobo/fastobo-py/issues)
[](https://f1000research.com/posters/8-1500)
[](https://pepy.tech/project/fastobo)
## Overview
[`fastobo`](https://crates.io/crates/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`](https://forge.rust-lang.org/other-installation-methods.html)
to learn how to install Rust on your machine.
Installation is then supported through `pip`:
```console
$ 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.
```python
import fastobo
obodoc = fastobo.load("../data/ms.obo")
```
Loading from a `gzip` file is supported:
```python
import fastobo
import gzip
gzdoc = fastobo.load(gzip.open("../data/cl.obo.gz"))
```
*Comments can be parsed but neither edited nor serialized, because of a limitation
with `pyo3` (the library used to generate the Python bindings). They are supported
in the Rust version of `fastobo`.*
## Feedback
Found a bug ? Have an enhancement request ? Head over to the
[GitHub issue tracker](https://github.com/fastobo/fastobo-py/issues) 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:
- Alex Henrie ([@alexhenrie](https://github.com/alexhenrie))
- Patrick Kalita ([@pkalita-lbl](https://github.com/pkalita-lbl))
## About
This project was developed by [Martin Larralde](https://github.com/althonos)
as part of a Master's Degree internship in the [BBOP team](http://berkeleybop.org/) of the
[Lawrence Berkeley National Laboratory](https://www.lbl.gov/), under the supervision of
[Chris Mungall](http://biosciences.lbl.gov/profiles/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](https://doi.org/10.7490/f1000research.1117405.1))
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"description": "# `fastobo-py` [](https://github.com/fastobo/fastobo-py/stargazers)\n\n*Faultless AST for Open Biomedical Ontologies in Python.*\n\n[](https://github.com/fastobo/fastobo-py/actions)\n[](https://codecov.io/gh/fastobo/fastobo-py)\n[](https://choosealicense.com/licenses/mit/)\n[](https://github.com/fastobo/fastobo-py/)\n[](https://pypi.org/project/fastobo)\n[](https://pypi.org/project/fastobo/#files)\n[](https://anaconda.org/bioconda/fastobo)\n[](https://pypi.org/project/fastobo/#files)\n[](https://pypi.org/project/fastobo/#files)\n[](https://github.com/fastobo/fastobo-py/blob/master/CHANGELOG.md)\n[](https://fastobo.readthedocs.io/)\n[](https://github.com/fastobo/fastobo-py/issues)\n[](https://f1000research.com/posters/8-1500)\n[](https://pepy.tech/project/fastobo)\n\n\n## Overview\n\n[`fastobo`](https://crates.io/crates/fastobo) is a Rust library implementing a\nreliable parser for the OBO file format 1.4. This extension module exports\nidiomatic Python bindings that can be used to load, edit and serialize ontologies\nin the OBO format.\n\n\n## Installation\n\nIf your platform has no pre-built binaries available, you will need to have the Rust\ncompiler installed. See the [documentation on `rust-lang.org`](https://forge.rust-lang.org/other-installation-methods.html)\nto learn how to install Rust on your machine.\n\nInstallation is then supported through `pip`:\n```console\n$ pip install fastobo --user\n```\n\n\n## Usage\n\nAn `OboDoc` instance can be instantiated from a path or from a binary file handle\nusing the `fastobo.load` function, or from a string using the `fastobo.loads` function.\n\n```python\nimport fastobo\nobodoc = fastobo.load(\"../data/ms.obo\")\n```\n\nLoading from a `gzip` file is supported:\n```python\nimport fastobo\nimport gzip\ngzdoc = fastobo.load(gzip.open(\"../data/cl.obo.gz\"))\n```\n\n*Comments can be parsed but neither edited nor serialized, because of a limitation\nwith `pyo3` (the library used to generate the Python bindings). They are supported\nin the Rust version of `fastobo`.*\n\n## Feedback\n\nFound a bug ? Have an enhancement request ? Head over to the\n[GitHub issue tracker](https://github.com/fastobo/fastobo-py/issues) of the project if\nyou need to report or ask something. If you are filling in on a bug, please include as much\ninformation as you can about the issue, and try to recreate the same bug in a simple, easily\nreproducible situation.\n\nThe following people have contributed to this project:\n\n- Alex Henrie ([@alexhenrie](https://github.com/alexhenrie))\n- Patrick Kalita ([@pkalita-lbl](https://github.com/pkalita-lbl))\n\n\n## About\n\nThis project was developed by [Martin Larralde](https://github.com/althonos)\nas part of a Master's Degree internship in the [BBOP team](http://berkeleybop.org/) of the\n[Lawrence Berkeley National Laboratory](https://www.lbl.gov/), under the supervision of\n[Chris Mungall](http://biosciences.lbl.gov/profiles/chris-mungall/). Cite this project as:\n\n*Larralde M.* **Developing Python and Rust libraries to improve the ontology ecosystem**\n*\\[version 1; not peer reviewed\\].* F1000Research 2019, 8(ISCB Comm J):1500 (poster)\n([https://doi.org/10.7490/f1000research.1117405.1](https://doi.org/10.7490/f1000research.1117405.1))\n",
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