trackhub.Hub
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Bases:
HubComponentRepresents a top-level track hub container.
- hubstr
Top-level name of the hub.
- short_labelstr
Short label for the hub, alias for UCSC parameter shortLabel.
- long_labelstr
Long label for the hub, alias for UCSC parameter longLabel. If None, will copy short_label.
- genomes_fileGenomesFile
If you already have a GenomesFile created, you can add it here; otherwise when one is created you’ll have to add one later with the add_genomes_file method.
- emailstr
Email that will be provided in the hub for contact info
- urlstr
Deprecated.
- filenamestr
If None, defaults to the value of hub plus “.hub.txt”. When uploaded, the filename is relative to the uploaded location.
Methods
__init__(hub[, short_label, long_label, ...])Represents a top-level track hub container.
add_child(child)Adds self as parent to child, and then adds child.
add_genomes_file(genomes_file)If a GenomesFile object was not provided upon instantiating this object, attach one now
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__(hub, short_label=None, long_label=None, genomes_file=None, genomes_filename=None, email='', url=None, filename=None)[source]
Represents a top-level track hub container.
- hubstr
Top-level name of the hub.
- short_labelstr
Short label for the hub, alias for UCSC parameter shortLabel.
- long_labelstr
Long label for the hub, alias for UCSC parameter longLabel. If None, will copy short_label.
- genomes_fileGenomesFile
If you already have a GenomesFile created, you can add it here; otherwise when one is created you’ll have to add one later with the add_genomes_file method.
- emailstr
Email that will be provided in the hub for contact info
- urlstr
Deprecated.
- filenamestr
If None, defaults to the value of hub plus “.hub.txt”. When uploaded, the filename is relative to the uploaded location.
- add_child(child)
Adds self as parent to child, and then adds child.
- add_genomes_file(genomes_file)[source]
If a GenomesFile object was not provided upon instantiating this object, attach one now
- 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.