API

gffutils

Create a database

create_db

Create a database from a GFF or GTF file.

Interact with a database

First, connect to an existing database:

FeatureDB

Then, use the methods of FeatureDB to interact:

FeatureDB.children	Return children of feature id.
FeatureDB.parents	Return parents of feature id.
FeatureDB.schema	Returns the database schema as a string.
FeatureDB.features_of_type	Returns an iterator of gffutils.Feature objects.
FeatureDB.count_features_of_type	Simple count of features.
FeatureDB.all_features	Iterate through the entire database.
FeatureDB.execute	Execute arbitrary queries on the db.
FeatureDB.featuretypes	Iterate over feature types found in the database.
FeatureDB.region	Return features within specified genomic coordinates.
FeatureDB.iter_by_parent_childs	For each parent of type featuretype, yield a list L of that parent and all of its children ([parent] + list(children)).

Modify a FeatureDB:

FeatureDB.update	Update the on-disk database with features in data.
FeatureDB.delete	Delete features from database.
FeatureDB.add_relation	Manually add relations to the database.
FeatureDB.set_pragmas	Set pragmas for the current database connection.

Operate on features:

FeatureDB.interfeatures	Construct new features representing the space between features.
FeatureDB.children_bp	Total bp of all children of a featuretype.
FeatureDB.merge	Merge features matching criteria together
FeatureDB.create_introns	Create introns from existing annotations.
FeatureDB.bed12	Converts feature into a BED12 format.

Feature objects

Most FeatureDB methods return Feature objects:

Feature

You can extract the sequence for a feature:

Feature.sequence

Retrieves the sequence of this feature as a string.

Creating a Feature object:

feature_from_line

Given a line from a GFF file, return a Feature object

Integration with other tools

gffutils.biopython_integration.to_seqfeature	Converts a gffutils.Feature object to a Bio.SeqFeature object.
gffutils.biopython_integration.from_seqfeature	Converts a Bio.SeqFeature object to a gffutils.Feature object.
gffutils.pybedtools_integration.tsses	Create 1-bp transcription start sites for all transcripts in the database and return as a sorted pybedtools.BedTool object pointing to a temporary file.
gffutils.pybedtools_integration.to_bedtool	Convert any iterator into a pybedtools.BedTool object.

Utilities

gffutils.helpers.asinterval	Converts a gffutils.Feature to a pybedtools.Interval
gffutils.helpers.merge_attributes	Merges two attribute dictionaries into a single dictionary.
gffutils.helpers.sanitize_gff_db	Sanitize given GFF db.
gffutils.helpers.annotate_gff_db	Annotate a GFF file by cross-referencing it with another GFF file, e.g. one containing gene models.
gffutils.helpers.infer_dialect	Infer the dialect based on the attributes.
gffutils.helpers.example_filename	Return the full path of a data file that ships with gffutils.
gffutils.inspect.inspect	Inspect a GFF or GTF data source.