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galaxy.visualization package

Package for Galaxy visualization plugins.

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.

__init__(chrom=None, start=0, end=0, sequence=None)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

static from_dict(obj_dict)[source]
static from_str(obj_str)[source]
class galaxy.visualization.genomes.Genome(key, description, len_file=None, twobit_file=None)[source]

Bases: object

Encapsulates information about a known genome/dbkey.

__init__(key, description, len_file=None, twobit_file=None)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

to_dict(num=None, chrom=None, low=None)[source]

Returns representation of self as a dictionary.

class galaxy.visualization.genomes.Genomes(app)[source]

Bases: object

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

__init__(app)[source]

x.__init__(…) initializes x; see help(type(x)) for signature

reload_genomes()[source]
check_and_reload()[source]
get_build(dbkey)[source]

Returns build for the given key.

get_dbkeys(trans, chrom_info=False, **kwd)[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.

has_reference_data(dbkey, dbkey_owner=None)[source]

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)[source]

Return reference data for a build.