fastobo

0.14.1 verified Fri May 01 auth: no python

Faultless AST for Open Biomedical Ontologies (OBO) in Python. Version 0.14.1 provides robust parsing, manipulation, and serialization of OBO files, with optional OWL export. Released regularly, with pre-built wheels for many platforms.

pip install fastobo

Common errors

error AttributeError: module 'fastobo' has no attribute 'load' ↓

cause Trying to use fastobo.load without importing it explicitly, or using an older version where load was not top-level.

fix

Use from fastobo import load

error TypeError: load() argument 1 must be str, not _io.TextIOWrapper ↓

cause Passing a file handle instead of a file path string.

fix

Call load with a file path string: doc = load('file.obo'); do not use open().

error ModuleNotFoundError: No module named 'fastobo' ↓

cause fastobo is not installed.

fix

pip install fastobo

error AttributeError: 'OboDoc' object has no attribute 'frames' ↓

cause OboDoc is iterable but does not have a 'frames' attribute; frames are accessed via iteration.

fix

Use for frame in doc: ...

Warnings

gotcha Some frame attributes (e.g., 'name') may be None if not defined in the OBO file. Always check for None before use. ↓

fix frame.name or ''

deprecated Support for Python 3.6 removed in v0.12.0; requires Python >=3.7. ↓

fix Upgrade Python to >=3.7

gotcha The OWL export functionality (dump_owl) is only available if the fastobo-owl dependency is installed (not included by default). ↓

fix pip install fastobo[owl] or pip install fastobo-owl

gotcha When loading from a file, the file must be a Path-like object or a string; streams are not supported directly. Use load(open(...)) may fail because load expects a filename or path string, not a file handle. ↓

fix doc = load('/path/to/file.obo') # Do not pass file handle

breaking In v0.12.0, the GIL is no longer released when loading from a file on Windows; this may affect performance but fixes compilation. ↓

fix No action needed unless relying on concurrency; upgrade to latest

Imports

OboDoc
```
from fastobo import OboDoc
```
No common wrong import; OboDoc is the main document class
load
```
from fastobo import load
```
Simple import, no common mistakes

Quickstart

Load and iterate over an OBO ontology file.

from fastobo import load

# Load an OBO file (use a test file or URL)
doc = load('go.obo')

# Iterate over all frames
for frame in doc:
    # Frames have an 'id' and 'name' attribute
    print(frame.id, frame.name)

# Convert to OWL (requires fastobo-owl, install separately)
# from fastobo import dump_owl
# dump_owl(doc, 'go.owl')