Warning

This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

galaxy.visualization.data_providers package

Galaxy visualization/visual analysis data providers.

Submodules

galaxy.visualization.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.

__init__(converted_dataset=None, original_dataset=None, dependencies=None, error_max_vals='Only the first %i values are returned.')[source]

Create basic data provider.

has_data(**kwargs)[source]

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

get_iterator(**kwargs)[source]

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

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.

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
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
__init__(original_dataset, max_lines_returned=30000)[source]
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.

galaxy.visualization.data_providers.cigar module

Functions for working with SAM/BAM CIGAR representation.

galaxy.visualization.data_providers.cigar.get_ref_based_read_seq_and_cigar(read_seq, read_start, ref_seq, ref_seq_start, cigar)[source]

Returns a ( new_read_seq, new_cigar ) that can be used with reference sequence to reconstruct the read. The new read sequence includes only bases that cannot be recovered from the reference: mismatches and insertions (soft clipped bases are not included). The new cigar replaces Ms with =s and Xs because the M operation can denote a sequence match or mismatch.

galaxy.visualization.data_providers.genome module

Data providers for genome visualizations.

galaxy.visualization.data_providers.genome.float_nan(n)[source]

Return None instead of NaN to pass jQuery 1.4’s strict JSON

galaxy.visualization.data_providers.genome.get_bounds(reads, start_pos_index, end_pos_index)[source]

Returns the minimum and maximum position for a set of reads.

class galaxy.visualization.data_providers.genome.FeatureLocationIndexDataProvider(converted_dataset)[source]

Bases: galaxy.visualization.data_providers.basic.BaseDataProvider

Reads/writes/queries feature location index (FLI) datasets.

__init__(converted_dataset)[source]
get_data(query)[source]
class galaxy.visualization.data_providers.genome.GenomeDataProvider(converted_dataset=None, original_dataset=None, dependencies=None, error_max_vals='Only the first %i %s in this region are displayed.')[source]

Bases: galaxy.visualization.data_providers.basic.BaseDataProvider

Base class for genome data providers. All genome providers use BED coordinate format (0-based, half-open coordinates) for both queries and returned data.

dataset_type = None

Mapping from column name to payload data; this mapping is used to create filters. Key is column name, value is a dict with mandatory key ‘index’ and optional key ‘name’. E.g. this defines column 4

col_name_data_attr_mapping = {4 : { index: 5, name: ‘Score’ } }

col_name_data_attr_mapping = {}
__init__(converted_dataset=None, original_dataset=None, dependencies=None, error_max_vals='Only the first %i %s in this region are displayed.')[source]
write_data_to_file(regions, filename)[source]

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

valid_chroms()[source]

Returns chroms/contigs that the dataset contains

has_data(chrom, start, end, **kwargs)[source]

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

open_data_file()[source]

Open data file for reading data.

get_iterator(data_file, chrom, start, end, **kwargs)[source]

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

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.

get_data(chrom=None, low=None, high=None, start_val=0, max_vals=9223372036854775807, **kwargs)[source]

Returns data in region defined by chrom, start, and end. start_val and max_vals are used to denote the data to return: 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_genome_data(chroms_info, **kwargs)[source]

Returns data for complete genome.

get_filters()[source]

Returns filters for provider’s data. Return value is a list of filters; each filter is a dictionary with the keys ‘name’, ‘index’, ‘type’. NOTE: This method uses the original dataset’s datatype and metadata to create the filters.

get_default_max_vals()[source]
class galaxy.visualization.data_providers.genome.FilterableMixin[source]
get_filters()[source]

Returns a dataset’s filters.

class galaxy.visualization.data_providers.genome.TabixDataProvider(converted_dataset=None, original_dataset=None, dependencies=None, error_max_vals='Only the first %i %s in this region are displayed.')[source]

Bases: galaxy.visualization.data_providers.genome.FilterableMixin, galaxy.visualization.data_providers.genome.GenomeDataProvider

dataset_type = 'tabix'

Tabix index data provider for the Galaxy track browser.

col_name_data_attr_mapping = {4: {'index': 4, 'name': 'Score'}}
open_data_file()[source]
get_iterator(data_file, chrom, start, end, **kwargs)[source]
write_data_to_file(regions, filename)[source]
class galaxy.visualization.data_providers.genome.IntervalDataProvider(converted_dataset=None, original_dataset=None, dependencies=None, error_max_vals='Only the first %i %s in this region are displayed.')[source]

Bases: galaxy.visualization.data_providers.genome.GenomeDataProvider

dataset_type = 'interval_index'

Processes interval data from native format to payload format.

Payload format: [ uid (offset), start, end, name, strand, thick_start, thick_end, blocks ]

get_iterator(data_file, chrom, start, end, **kwargs)[source]
process_data(iterator, start_val=0, max_vals=None, **kwargs)[source]

Provides

write_data_to_file(regions, filename)[source]
class galaxy.visualization.data_providers.genome.IntervalTabixDataProvider(converted_dataset=None, original_dataset=None, dependencies=None, error_max_vals='Only the first %i %s in this region are displayed.')[source]

Bases: galaxy.visualization.data_providers.genome.TabixDataProvider, galaxy.visualization.data_providers.genome.IntervalDataProvider

Provides data from a BED file indexed via tabix.

class galaxy.visualization.data_providers.genome.BedDataProvider(converted_dataset=None, original_dataset=None, dependencies=None, error_max_vals='Only the first %i %s in this region are displayed.')[source]

Bases: galaxy.visualization.data_providers.genome.GenomeDataProvider

Processes BED data from native format to payload format.

Payload format: [ uid (offset), start, end, name, strand, thick_start, thick_end, blocks ]

dataset_type = 'interval_index'
get_iterator(data_file, chrom, start, end, **kwargs)[source]
process_data(iterator, start_val=0, max_vals=None, **kwargs)[source]

Provides

write_data_to_file(regions, filename)[source]
class galaxy.visualization.data_providers.genome.BedTabixDataProvider(converted_dataset=None, original_dataset=None, dependencies=None, error_max_vals='Only the first %i %s in this region are displayed.')[source]

Bases: galaxy.visualization.data_providers.genome.TabixDataProvider, galaxy.visualization.data_providers.genome.BedDataProvider

Provides data from a BED file indexed via tabix.

class galaxy.visualization.data_providers.genome.RawBedDataProvider(converted_dataset=None, original_dataset=None, dependencies=None, error_max_vals='Only the first %i %s in this region are displayed.')[source]

Bases: galaxy.visualization.data_providers.genome.BedDataProvider

Provide data from BED file.

NOTE: this data provider does not use indices, and hence will be very slow for large datasets.

get_iterator(data_file, chrom=None, start=None, end=None, **kwargs)[source]
class galaxy.visualization.data_providers.genome.VcfDataProvider(converted_dataset=None, original_dataset=None, dependencies=None, error_max_vals='Only the first %i %s in this region are displayed.')[source]

Bases: galaxy.visualization.data_providers.genome.GenomeDataProvider

Abstract class that processes VCF data from native format to payload format.

Payload format: An array of entries for each locus in the file. Each array has the following entries:

  1. GUID (unused)
  2. location (0-based)
  3. reference base(s)
  4. alternative base(s)
  5. quality score
  6. whether variant passed filter
  7. sample genotypes – a single string with samples separated by commas; empty string denotes the reference genotype

8-end: allele counts for each alternative

col_name_data_attr_mapping = {'Qual': {'index': 6, 'name': 'Qual'}}
dataset_type = 'variant'
process_data(iterator, start_val=0, max_vals=None, **kwargs)[source]

Returns a dict with the following attributes:

data - a list of variants with the format

.. raw:: text

    [<guid>, <start>, <end>, <name>, cigar, seq]

message - error/informative message
write_data_to_file(regions, filename)[source]
class galaxy.visualization.data_providers.genome.VcfTabixDataProvider(converted_dataset=None, original_dataset=None, dependencies=None, error_max_vals='Only the first %i %s in this region are displayed.')[source]

Bases: galaxy.visualization.data_providers.genome.TabixDataProvider, galaxy.visualization.data_providers.genome.VcfDataProvider

Provides data from a VCF file indexed via tabix.

dataset_type = 'variant'
class galaxy.visualization.data_providers.genome.RawVcfDataProvider(converted_dataset=None, original_dataset=None, dependencies=None, error_max_vals='Only the first %i %s in this region are displayed.')[source]

Bases: galaxy.visualization.data_providers.genome.VcfDataProvider

Provide data from VCF file.

NOTE: this data provider does not use indices, and hence will be very slow for large datasets.

open_data_file()[source]
get_iterator(data_file, chrom, start, end, **kwargs)[source]
class galaxy.visualization.data_providers.genome.BamDataProvider(converted_dataset=None, original_dataset=None, dependencies=None, error_max_vals='Only the first %i %s in this region are displayed.')[source]

Bases: galaxy.visualization.data_providers.genome.GenomeDataProvider, galaxy.visualization.data_providers.genome.FilterableMixin

Provides access to intervals from a sorted indexed BAM file. Coordinate data is reported in BED format: 0-based, half-open.

dataset_type = 'bai'
get_filters()[source]

Returns filters for dataset.

write_data_to_file(regions, filename)[source]

Write reads in regions to file.

open_data_file()[source]
get_iterator(data_file, chrom, start, end, **kwargs)[source]

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

process_data(iterator, start_val=0, max_vals=None, ref_seq=None, iterator_type='nth', mean_depth=None, start=0, end=0, **kwargs)[source]

Returns a dict with the following attributes:

data - a list of reads with the format
    [<guid>, <start>, <end>, <name>, <read_1>, <read_2>, [empty], <mapq_scores>]

    where <read_1> has the format
        [<start>, <end>, <cigar>, <strand>, <read_seq>]

    and <read_2> has the format
        [<start>, <end>, <cigar>, <strand>, <read_seq>]

    Field 7 is empty so that mapq scores' location matches that in single-end reads.
    For single-end reads, read has format:
        [<guid>, <start>, <end>, <name>, <cigar>, <strand>, <seq>, <mapq_score>]

    NOTE: read end and sequence data are not valid for reads outside of
    requested region and should not be used.

max_low - lowest coordinate for the returned reads
max_high - highest coordinate for the returned reads
message - error/informative message
class galaxy.visualization.data_providers.genome.SamDataProvider(converted_dataset=None, original_dataset=None, dependencies=None)[source]

Bases: galaxy.visualization.data_providers.genome.BamDataProvider

dataset_type = 'bai'
__init__(converted_dataset=None, original_dataset=None, dependencies=None)[source]

Create SamDataProvider.

class galaxy.visualization.data_providers.genome.BBIDataProvider(converted_dataset=None, original_dataset=None, dependencies=None, error_max_vals='Only the first %i %s in this region are displayed.')[source]

Bases: galaxy.visualization.data_providers.genome.GenomeDataProvider

BBI data provider for the Galaxy track browser.

dataset_type = 'bigwig'
valid_chroms()[source]
has_data(chrom)[source]
get_data(chrom, start, end, start_val=0, max_vals=None, num_samples=1000, **kwargs)[source]
class galaxy.visualization.data_providers.genome.BigBedDataProvider(converted_dataset=None, original_dataset=None, dependencies=None, error_max_vals='Only the first %i %s in this region are displayed.')[source]

Bases: galaxy.visualization.data_providers.genome.BBIDataProvider

class galaxy.visualization.data_providers.genome.BigWigDataProvider(converted_dataset=None, original_dataset=None, dependencies=None, error_max_vals='Only the first %i %s in this region are displayed.')[source]

Bases: galaxy.visualization.data_providers.genome.BBIDataProvider

Provides data from BigWig files; position data is reported in 1-based coordinate system, i.e. wiggle format.

class galaxy.visualization.data_providers.genome.IntervalIndexDataProvider(converted_dataset=None, original_dataset=None, dependencies=None, error_max_vals='Only the first %i %s in this region are displayed.')[source]

Bases: galaxy.visualization.data_providers.genome.FilterableMixin, galaxy.visualization.data_providers.genome.GenomeDataProvider

Interval index files used for GFF, Pileup files.

col_name_data_attr_mapping = {4: {'index': 4, 'name': 'Score'}}
dataset_type = 'interval_index'
write_data_to_file(regions, filename)[source]
open_data_file()[source]
get_iterator(data_file, chrom, start, end, **kwargs)[source]

Returns an iterator for data in data_file in chrom:start-end

process_data(iterator, start_val=0, max_vals=None, **kwargs)[source]
class galaxy.visualization.data_providers.genome.RawGFFDataProvider(converted_dataset=None, original_dataset=None, dependencies=None, error_max_vals='Only the first %i %s in this region are displayed.')[source]

Bases: galaxy.visualization.data_providers.genome.GenomeDataProvider

Provide data from GFF file that has not been indexed.

NOTE: this data provider does not use indices, and hence will be very slow for large datasets.

dataset_type = 'interval_index'
get_iterator(data_file, chrom, start, end, **kwargs)[source]

Returns an iterator that provides data in the region chrom:start-end as well as a file offset.

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.

class galaxy.visualization.data_providers.genome.GtfTabixDataProvider(converted_dataset=None, original_dataset=None, dependencies=None, error_max_vals='Only the first %i %s in this region are displayed.')[source]

Bases: galaxy.visualization.data_providers.genome.TabixDataProvider

Returns data from GTF datasets that are indexed via tabix.

process_data(iterator, start_val=0, max_vals=None, **kwargs)[source]
class galaxy.visualization.data_providers.genome.ENCODEPeakDataProvider(converted_dataset=None, original_dataset=None, dependencies=None, error_max_vals='Only the first %i %s in this region are displayed.')[source]

Bases: galaxy.visualization.data_providers.genome.GenomeDataProvider

Abstract class that processes ENCODEPeak data from native format to payload format.

Payload format: [ uid (offset), start, end, name, strand, thick_start, thick_end, blocks ]

get_iterator(data_file, chrom, start, end, **kwargs)[source]
process_data(iterator, start_val=0, max_vals=None, **kwargs)[source]

Provides

class galaxy.visualization.data_providers.genome.ENCODEPeakTabixDataProvider(converted_dataset=None, original_dataset=None, dependencies=None, error_max_vals='Only the first %i %s in this region are displayed.')[source]

Bases: galaxy.visualization.data_providers.genome.TabixDataProvider, galaxy.visualization.data_providers.genome.ENCODEPeakDataProvider

Provides data from an ENCODEPeak dataset indexed via tabix.

get_filters()[source]

Returns filters for dataset.

class galaxy.visualization.data_providers.genome.ChromatinInteractionsDataProvider(converted_dataset=None, original_dataset=None, dependencies=None, error_max_vals='Only the first %i %s in this region are displayed.')[source]

Bases: galaxy.visualization.data_providers.genome.GenomeDataProvider

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

Provides

get_default_max_vals()[source]
class galaxy.visualization.data_providers.genome.ChromatinInteractionsTabixDataProvider(converted_dataset=None, original_dataset=None, dependencies=None, error_max_vals='Only the first %i %s in this region are displayed.')[source]

Bases: galaxy.visualization.data_providers.genome.TabixDataProvider, galaxy.visualization.data_providers.genome.ChromatinInteractionsDataProvider

get_iterator(data_file, chrom, start=0, end=9223372036854775807, interchromosomal=False, **kwargs)[source]
galaxy.visualization.data_providers.genome.package_gff_feature(feature, no_detail=False, filter_cols=[])[source]

Package a GFF feature in an array for data providers.

galaxy.visualization.data_providers.registry module

class galaxy.visualization.data_providers.registry.DataProviderRegistry[source]

Bases: object

Registry for data providers that enables listing and lookup.

__init__()[source]
get_data_provider(trans, name=None, source='data', raw=False, original_dataset=None)[source]

Returns data provider matching parameter values. For standalone data sources, source parameter is ignored.