galaxy.visualization package

Package for Galaxy visualization plugins.

Subpackages

• galaxy.visualization.data_providers package
  • Subpackages
    • galaxy.visualization.data_providers.phyloviz package
      • Submodules
      • galaxy.visualization.data_providers.phyloviz.baseparser module
      • galaxy.visualization.data_providers.phyloviz.newickparser module
      • galaxy.visualization.data_providers.phyloviz.nexusparser module
      • galaxy.visualization.data_providers.phyloviz.phyloxmlparser module
  • Submodules
  • galaxy.visualization.data_providers.basic module
  • galaxy.visualization.data_providers.cigar module
  • galaxy.visualization.data_providers.genome module
  • galaxy.visualization.data_providers.registry module
• galaxy.visualization.genome package
• galaxy.visualization.plugins package
  • Submodules
  • galaxy.visualization.plugins.config_parser module
  • galaxy.visualization.plugins.interactive_environments module
  • galaxy.visualization.plugins.plugin module
  • galaxy.visualization.plugins.registry module
  • galaxy.visualization.plugins.resource_parser module
  • galaxy.visualization.plugins.utils module
• galaxy.visualization.tracks package

Submodules

galaxy.visualization.genomes module

galaxy.visualization.genomes.decode_dbkey(dbkey)

Decodes dbkey and returns tuple ( username, dbkey )

class galaxy.visualization.genomes.GenomeRegion(chrom=None, start=0, end=0, sequence=None)

Bases: object

A genomic region on an individual chromosome.

__init__(chrom=None, start=0, end=0, sequence=None)

Initialize self. See help(type(self)) for accurate signature.

static from_dict(obj_dict)

static from_str(obj_str)

class galaxy.visualization.genomes.Genome(key, description, len_file=None, twobit_file=None)

Bases: object

Encapsulates information about a known genome/dbkey.

__init__(key, description, len_file=None, twobit_file=None)

Initialize self. See help(type(self)) for accurate signature.

to_dict(num=None, chrom=None, low=None)

Returns representation of self as a dictionary.

class galaxy.visualization.genomes.Genomes(app: galaxy.structured_app.MinimalManagerApp)

Bases: object

Provides information about available genome data and methods for manipulating that data.

__init__(app: galaxy.structured_app.MinimalManagerApp)

Initialize self. See help(type(self)) for accurate signature.

reload_genomes()

check_and_reload()

get_build(dbkey)

Returns build for the given key.

get_dbkeys(user, chrom_info=False)

Returns all known dbkeys. If chrom_info is True, only dbkeys with chromosome lengths are returned.

chroms(trans, dbkey=None, num=None, chrom=None, low=None)

Returns a naturally sorted list of chroms/contigs for a given dbkey. Use either chrom or low to specify the starting chrom in the return list.

has_reference_data(dbkey, dbkey_owner=None)

Returns true if there is reference data for the specified dbkey. If dbkey is custom, dbkey_owner is needed to determine if there is reference data.

reference(trans, dbkey, chrom, low, high)

Return reference data for a build.