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¶
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galaxy.visualization.genomes.
decode_dbkey
(dbkey)[source]¶ Decodes dbkey and returns tuple ( username, dbkey )
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class
galaxy.visualization.genomes.
GenomeRegion
(chrom=None, start=0, end=0, sequence=None)[source]¶ Bases:
object
A genomic region on an individual chromosome.
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class
galaxy.visualization.genomes.
Genome
(key, description, len_file=None, twobit_file=None)[source]¶ Bases:
object
Encapsulates information about a known genome/dbkey.
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class
galaxy.visualization.genomes.
Genomes
(app)[source]¶ Bases:
object
Provides information about available genome data and methods for manipulating that data.
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get_dbkeys
(trans, chrom_info=False, **kwd)[source]¶ Returns all known dbkeys. If chrom_info is True, only dbkeys with chromosome lengths are returned.
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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.
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