trackhub.GroupsFile

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class trackhub.GroupsFile(groups, filename=None)

Bases: HubComponent

Represents the groups file on disk, used for assembly hubs.

Parameters

• groups (list) – List of GroupDefinition objects

• filename (str) – Filename to use, relative to the top-level hub. If None, default is to use “<genome>/groups.txt”

Methods

__init__(groups[, filename])	Represents the groups file on disk, used for assembly hubs.
add_child(child)	Adds self as parent to child, and then adds child.
add_groups(groups)	Add a list of GroupDefinition objects.
add_parent(parent)	Adds self as child of parent, then adds parent.
leaves(cls[, level, intermediate])	Returns an iterator of the HubComponent leaves that are of class cls.
makedirs(fn)
render([staging])	Renders the object to file, returning a list of created files.
root([cls, level])	Returns the top-most HubComponent in the hierarchy.
validate()	Runs validation, raising exceptions as needed.

__init__(groups, filename=None)

Represents the groups file on disk, used for assembly hubs.

Parameters

• groups (list) – List of GroupDefinition objects

• filename (str) – Filename to use, relative to the top-level hub. If None, default is to use “<genome>/groups.txt”

add_child(child)

Adds self as parent to child, and then adds child.

add_groups(groups)

Add a list of GroupDefinition objects.

Parameters

groups (list) – List of GroupDefinition objects.

add_parent(parent)

Adds self as child of parent, then adds parent.

leaves(cls, level=0, intermediate=False)

Returns an iterator of the HubComponent leaves that are of class cls.

If intermediate is True, then return any intermediate classes as well.

render(staging=None)

Renders the object to file, returning a list of created files.

Calls validation code, and, as long as each child is also a subclass of HubComponent, the rendering is recursive.

root(cls=None, level=0)

Returns the top-most HubComponent in the hierarchy.

If cls is not None, then return the top-most attribute HubComponent that is an instance of class cls.

For a fully-constructed track hub (and cls=None), this should return a a Hub object for every component in the hierarchy.

validate()

Runs validation, raising exceptions as needed. Must be overridden by subclass.