data_providers Package

data_providers Package

Galaxy visualization/visual analysis data providers.

basic Module

class galaxy.visualization.data_providers.basic.BaseDataProvider(converted_dataset=None, original_dataset=None, dependencies=None, error_max_vals='Only the first %i values are returned.')[source]

Bases: object

Base class for data providers. Data providers (a) read and package data from datasets; and (b) write subsets of data to new datasets.

get_data(chrom, start, end, start_val=0, max_vals=9223372036854775807, **kwargs)[source]

Returns data as specified by kwargs. start_val is the first element to return and max_vals indicates the number of values to return.

Return value must be a dictionary with the following attributes:
dataset_type, data
get_iterator(**kwargs)[source]

Returns an iterator that provides data in the region chrom:start-end

has_data(**kwargs)[source]

Returns true if dataset has data in the specified genome window, false otherwise.

process_data(iterator, start_val=0, max_vals=None, **kwargs)[source]

Process data from an iterator to a format that can be provided to client.

write_data_to_file(filename, **kwargs)[source]

Write data in region defined by chrom, start, and end to a file.

class galaxy.visualization.data_providers.basic.ColumnDataProvider(original_dataset, max_lines_returned=30000)[source]

Bases: galaxy.visualization.data_providers.basic.BaseDataProvider

Data provider for columnar data

MAX_LINES_RETURNED = 30000
get_data(columns=None, start_val=0, max_vals=None, skip_comments=True, **kwargs)[source]

Returns data from specified columns in dataset. Format is list of lists where each list is a line of data.

genome Module

registry Module