trackhub.Assembly

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class trackhub.Assembly(genome, twobit_file=None, groups=None, trackdb=None, genome_file_obj=None, html_string=None, html_string_format='rst', **kwargs)

Bases: Genome

Represents a genome stanza within a “genomes.txt” file for a non-UCSC genome.

The file itself is represented by a GenomesFile object.

Parameters:

• genome (str) – The genome assembly name to use for this assembly

• twobit_file (str) – Local path to 2bit file.

Methods

__init__(genome[, twobit_file, groups, ...])	Represents a genome stanza within a "genomes.txt" file for a non-UCSC genome.
add_child(child)	Adds self as parent to child, and then adds child.
add_groups(groups)
add_params(**kw)	Add [possibly many] parameters to the Assembly.
add_parent(parent)	Adds self as child of parent, then adds parent.
add_trackdb(trackdb)
add_twobit(twobit)
leaves(cls[, level, intermediate])	Returns an iterator of the HubComponent leaves that are of class cls.
makedirs(fn)
remove_params(*args)	Remove [possibly many] parameters from the Assembly.
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__(genome, twobit_file=None, groups=None, trackdb=None, genome_file_obj=None, html_string=None, html_string_format='rst', **kwargs)

Represents a genome stanza within a “genomes.txt” file for a non-UCSC genome.

The file itself is represented by a GenomesFile object.

Parameters:

• genome (str) – The genome assembly name to use for this assembly

• twobit_file (str) – Local path to 2bit file.

add_child(child)

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

add_params(**kw)

Add [possibly many] parameters to the Assembly.

Parameters will be checked against known UCSC parameters and their supported formats.

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.

remove_params(*args)

Remove [possibly many] parameters from the Assembly.

E.g.,

remove_params(‘color’, ‘visibility’)

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.