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galaxy.visualization package¶
Package for Galaxy visualization plugins.
Subpackages¶
- galaxy.visualization.data_providers package
- Subpackages
- Submodules
- galaxy.visualization.data_providers.basic module
- galaxy.visualization.data_providers.cigar module
- galaxy.visualization.data_providers.genome module
float_nan()
get_bounds()
FeatureLocationIndexDataProvider
GenomeDataProvider
GenomeDataProvider.dataset_type
GenomeDataProvider.col_name_data_attr_mapping
GenomeDataProvider.__init__()
GenomeDataProvider.write_data_to_file()
GenomeDataProvider.valid_chroms()
GenomeDataProvider.has_data()
GenomeDataProvider.open_data_file()
GenomeDataProvider.get_iterator()
GenomeDataProvider.process_data()
GenomeDataProvider.get_data()
GenomeDataProvider.get_genome_data()
GenomeDataProvider.get_filters()
GenomeDataProvider.get_default_max_vals()
FilterableMixin
TabixDataProvider
IntervalDataProvider
IntervalTabixDataProvider
BedDataProvider
BedTabixDataProvider
RawBedDataProvider
VcfDataProvider
VcfTabixDataProvider
RawVcfDataProvider
BamDataProvider
SamDataProvider
BBIDataProvider
BigBedDataProvider
BigWigDataProvider
IntervalIndexDataProvider
IntervalIndexDataProvider.col_name_data_attr_mapping
IntervalIndexDataProvider.dataset_type
IntervalIndexDataProvider.write_data_to_file()
IntervalIndexDataProvider.open_data_file()
IntervalIndexDataProvider.get_iterator()
IntervalIndexDataProvider.process_data()
IntervalIndexDataProvider.original_dataset
RawGFFDataProvider
GtfTabixDataProvider
ENCODEPeakDataProvider
ENCODEPeakTabixDataProvider
ChromatinInteractionsDataProvider
ChromatinInteractionsTabixDataProvider
package_gff_feature()
- galaxy.visualization.data_providers.registry module
- galaxy.visualization.genome package
- galaxy.visualization.plugins package
- Submodules
- galaxy.visualization.plugins.config_parser module
- galaxy.visualization.plugins.plugin module
- galaxy.visualization.plugins.registry module
VisualizationsRegistry
VisualizationsRegistry.BASE_URL
VisualizationsRegistry.TEMPLATE_PATHS_CONFIG
VisualizationsRegistry.BUILT_IN_VISUALIZATIONS
VisualizationsRegistry.__init__()
VisualizationsRegistry.get_plugin()
VisualizationsRegistry.get_plugins()
VisualizationsRegistry.get_visualizations()
VisualizationsRegistry.get_visualization()
VisualizationsRegistry.is_object_applicable()
- 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)[source]¶
Decodes dbkey and returns tuple ( username, dbkey )
- class galaxy.visualization.genomes.GenomeRegion(chrom=None, start=0, end=0, sequence=None)[source]¶
Bases:
object
A genomic region on an individual chromosome.
- class galaxy.visualization.genomes.Genome(key, description, len_file=None, twobit_file=None)[source]¶
Bases:
object
Encapsulates information about a known genome/dbkey.
- class galaxy.visualization.genomes.Genomes(app: StructuredApp)[source]¶
Bases:
object
Provides information about available genome data and methods for manipulating that data.
- __init__(app: StructuredApp)[source]¶
- get_dbkeys(user, chrom_info=False)[source]¶
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)[source]¶
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.