galaxy.visualization package¶
Package for Galaxy visualization plugins.
Subpackages¶
- galaxy.visualization.data_providers package
- galaxy.visualization.genome package
- galaxy.visualization.plugins package
- 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.