.. _api:
.. rst-class:: html-toggle
API
===
`gffutils`
----------
.. automodule:: gffutils
:members:
Create a database
-----------------
.. currentmodule:: gffutils.create
.. autosummary::
:toctree: autodocs
:nosignatures:
create_db
Interact with a database
------------------------
First, connect to an existing database:
.. currentmodule:: gffutils.interface
.. autosummary::
:toctree: autodocs
:nosignatures:
FeatureDB
Then, use the methods of :class:`FeatureDB` to interact:
.. autosummary::
:toctree: autodocs
:nosignatures:
FeatureDB.children
FeatureDB.parents
FeatureDB.schema
FeatureDB.features_of_type
FeatureDB.count_features_of_type
FeatureDB.all_features
FeatureDB.execute
FeatureDB.featuretypes
FeatureDB.region
FeatureDB.iter_by_parent_childs
Modify a :class:`FeatureDB`:
.. autosummary::
:toctree: autodocs
:nosignatures:
FeatureDB.update
FeatureDB.delete
FeatureDB.add_relation
FeatureDB.set_pragmas
Operate on features:
.. autosummary::
:toctree: autodocs
:nosignatures:
FeatureDB.interfeatures
FeatureDB.children_bp
FeatureDB.merge
FeatureDB.create_introns
FeatureDB.bed12
Feature objects
---------------
Most :class:`FeatureDB` methods return :class:`Feature` objects:
.. currentmodule:: gffutils.feature
.. autosummary::
:toctree: autodocs
:nosignatures:
Feature
You can extract the sequence for a feature:
.. autosummary::
:toctree: autodocs
:nosignatures:
Feature.sequence
Creating a :class:`Feature` object:
.. autosummary::
:toctree: autodocs
:nosignatures:
feature_from_line
Integration with other tools
----------------------------
.. currentmodule:: gffutils
.. autosummary::
:toctree: autodocs
:nosignatures:
gffutils.biopython_integration.to_seqfeature
gffutils.biopython_integration.from_seqfeature
gffutils.pybedtools_integration.tsses
gffutils.pybedtools_integration.to_bedtool
Utilities
---------
.. autosummary::
:toctree: autodocs
:nosignatures:
gffutils.helpers.asinterval
gffutils.helpers.merge_attributes
gffutils.helpers.sanitize_gff_db
gffutils.helpers.annotate_gff_db
gffutils.helpers.infer_dialect
gffutils.helpers.example_filename
gffutils.inspect.inspect