BioMart.jl

Query(dataset::Dataset, args...)

Build a Query for the given Dataset and combination of Filters and Attributes. An Interval from GenomicFeatures can also be provided to filter by genomic position.

A Query build the request in XML format but does not execute it. To do so you can call BioMart.execute or directly call the Query object.

To build and execute a Query at once use BioMart.query.

Example:

q = BioMart.Query(
    BioMart.Dataset("maj_gene_ensembl"),
    Interval("1", 1, 200000),
    BioMart.Attribute("external_gene_name"),
    BioMart.Attributes("ensembl_gene_id", "ensembl_transcript_id", "strand"),
    BioMart.Filter(strand = "1")
)
q() #BioMart.execute(q)

execute(q::Query)

Exectute a Query and returns a DataFrame with the results.

query(args...)

Build a Query using args, exectute it immediately and returns the results.

struct Attribute
    name::String
end

Specify an attribute to be returned by the query.

Example :

BioMart.Attribute("external_gene_name")

Attributes(args...)

Specify a list of attributes to be returned by the query.

Example :

BioMart.Attributes(
    "external_gene_name",
    "strand"
)

struct Filter
    name::String
    value::String
end

Specify a filter to be applied to the query.

Examples :

BioMart.Filter(ensembl_gene_id = "ENSG00000146648")
BioMart.Filter("ensembl_gene_id", "ENSG00000146648")

BioMart.Filters(;args...)

Specify a list of filters to be applied to the query.

Example :

BioMart.Filters(
    ensembl_gene_id = "ENSG00000146648", 
    chromosome_name = "7"
)

BioMart.databases()

List the available databases.

go recursively over the XML and collect AttributeDescriptions

BioMart.datasets(database::Database)
BioMart.datasets(database::String)

List the datasets available for a given database.

Examples :

BioMart.datasets("ENSEMBL_MART_ENSEMBL")

dbs = BioMart.databases()
BioMart.datasets(dbs[1])

BioMart.list_attributes(dataset::Dataset)
BioMart.list_attributes(dataset::String)

List the attributes available for a given dataset.

Examples :

BioMart.list_attributes("hsapiens_gene_ensembl")