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Contents
require 'rbbt-util'
require 'rbbt/resource'
require 'rbbt/sources/organism'
module MSigDB
extend Resource
self.subdir = 'share/databases/MSigDB'
def self.organism(org="Hsa")
Organism.default_code(org)
end
#self.search_paths = {}
#self.search_paths[:default] = :lib
MSigDB.claim MSigDB['.source/all_sets.zip'], :proc do |filename|
raise "Download the 'ZIPed file set' from http://software.broadinstitute.org/gsea/downloads.jsp into #{filename}"
end
MSigDB.claim MSigDB.all_sets, :proc do |dirname|
zip_file = MSigDB['.source/all_sets.zip'].produce.find
TmpFile.with_dir do |tmpdir|
Misc.unzip_in_dir(zip_file, tmpdir)
Path.setup(tmpdir)
tmpdir.glob('**/*symbols.gmt').each do |file|
name_parts = File.basename(file).split(".")
base_name = name_parts[0..-5] * "_"
dumper = TSV::Dumper.new :key_field => "MSigDB Geneset ID", :fields => ["Associated Gene Name"], :namespace => MSigDB.organism, :type => :flat
dumper.init
io = TSV.traverse file, :type => :array, :into => dumper do |line|
name, url, *genes = line.split("\t")
[name, genes]
end
Open.write(dirname[base_name], io.stream)
end
end
end
end
if defined? Entity
module MSigDBGeneSet
extend Entity
self.format= "MSigDB Geneset ID"
property :name => :single2array do
self.downcase.gsub("_",' ')
end
property :genes => :single2array do
@@pathway_genes ||= MSigDB.all_sets.msigdb.tsv :persist => true
genes = @@pathway_genes[self]
Gene.setup(genes, "Associated Gene Name", MSigDB.organism).ensembl
end
end
end
Version data entries
66 entries across 66 versions & 1 rubygems