Warning

This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

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)

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)

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

Returns representation of self as a dictionary.

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

Bases: object

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

__init__(app: galaxy.structured_app.StructuredApp)

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.