Module: BioMart
- Defined in:
- lib/rbbt/sources/biomart.rb
Overview
This module interacts with BioMart. It performs queries to BioMart and synthesises a hash with the results. Note that this module connects to the online BioMart WS using the Open in ‘rbbt/util/open’ module which offers caching by default. To obtain up to date results you may need to clear the cache from previous queries.
Defined Under Namespace
Classes: QueryError
Constant Summary collapse
- BIOMART_URL =
'http://biomart.org/biomart/martservice?query='
- MISSING_IN_ARCHIVE =
Rbbt.etc.biomart.missing_in_archive.exists? ? Rbbt.etc.biomart.missing_in_archive.yaml : {}
Class Method Summary collapse
-
.query(database, main, attrs = nil, filters = nil, data = nil, open_options = {}) ⇒ Object
This method performs a query in biomart for a datasets and a given set of attributes, there must be a main attribute that will be used as the key in the result hash, optionally there may be a list of additional attributes and filters.
- .tsv(database, main, attrs = nil, filters = nil, data = nil, open_options = {}) ⇒ Object
Class Method Details
.query(database, main, attrs = nil, filters = nil, data = nil, open_options = {}) ⇒ Object
This method performs a query in biomart for a datasets and a given set of attributes, there must be a main attribute that will be used as the key in the result hash, optionally there may be a list of additional attributes and filters. The data parameter at the end is used internally to incrementally building the result, due to a limitation of the BioMart WS that only allows 3 external arguments, users normally should leave it unspecified or nil. The result is a hash, where the keys are the different values for the main attribute, and the value is a hash with every other attribute as key, and as value and array with all possible values (Note that for a given value of the main attribute, there may be more than one value for another attribute). If filters is left a nil it adds a filter to the BioMart query to remove results with the main attribute empty, this may cause an error if the BioMart WS does not allow filtering with that attribute.
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# File 'lib/rbbt/sources/biomart.rb', line 136 def self.query(database, main, attrs = nil, filters = nil, data = nil, = {}) = Misc.add_defaults , :nocache => false, :filename => nil, :field_names => nil, :by_chr => false filename, field_names, by_chr = Misc. , :filename, :field_names, :by_chr attrs ||= [] = Misc.add_defaults , :keep_empty => false, :merge => true Log.low "BioMart query: '#{main}' [#{(attrs || []) * ', '}] [#{(filters || []) * ', '}] #{.inspect}" max_items = 2 chunks = [] chunk = [] attrs.each{|a| chunk << a if chunk.length == max_items chunks << chunk chunk = [] end } chunks << chunk if chunk.any? chunks << [] if chunks.empty? Log.low "Chunks: #{chunks.length}" if chunks.any? chunks.each_with_index{|chunk,i| Log.low "Chunk #{ i + 1 } / #{chunks.length}: [#{chunk * ", "}]" data = get(database, main, chunk, filters, data, ) } else data = get(database, main, [], filters, data, ) end [:filename] ||= "BioMart[#{main}+#{attrs.length}]" if filename.nil? results = TSV.open data, results.key_field = main results.fields = attrs results else Open.write(filename) do |f| f.puts "#: " << Misc.hash2string(TSV::ENTRIES.collect{|key| [key, [key]]}) if field_names.nil? f.puts "#" << [main, attrs].flatten * "\t" else f.puts "#" << field_names * "\t" end f.write Open.read(data) end FileUtils.rm data filename end end |
.tsv(database, main, attrs = nil, filters = nil, data = nil, open_options = {}) ⇒ Object
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# File 'lib/rbbt/sources/biomart.rb', line 191 def self.tsv(database, main, attrs = nil, filters = nil, data = nil, = {}) attrs ||= [] if @archive_url attrs = attrs.reject{|attr| (MISSING_IN_ARCHIVE[@archive] || []).include? attr[1]} end codes = attrs.collect{|attr| attr[1]} if [:filename].nil? tsv = query(database, main.last, codes, filters, data, ) tsv.key_field = main.first tsv.fields = attrs.collect{|attr| attr.first} tsv else query(database, main.last, codes, filters, data, .merge(:field_names => [main.first, attrs.collect{|attr| attr.first}].flatten)) end end |