Sha256: 320d93396a49827f003c038f67070d6b63f3b2e002dd032037b88dc310a71cef
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Size: 1.54 KB
Versions: 36
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Contents
require 'rbbt-util'
require 'rbbt/resource'
module Intogen
extend Resource
self.subdir = 'share/databases/Intogen'
#def self.organism(org="Hsa")
# Organism.default_code(org)
#end
#self.search_paths = {}
#self.search_paths[:default] = :lib
Intogen.claim Intogen['.source']["intogen_driver_mutations_catalog.zip"], :proc do |filename|
raise "Download the fila at 'https://www.intogen.org/downloads?file=/repository/downloads/intogen_driver_mutations_catalog-2016.5.zip' into '#{filename}'"
end
Intogen.claim Intogen.driver_mutations_catalog, :proc do |filaname|
all_tsv = nil
TmpFile.with_file do |tmpdir|
Open.mkdir tmpdir
Misc.in_dir tmpdir do
`unzip '#{Intogen['.source']["intogen_driver_mutations_catalog.zip"].produce.find}'`
Dir.glob("./*/mutation_analysis.tsv").each do |file|
cohort = File.basename(File.dirname(file))
parser = TSV::Parser.new file, :header_hash => '', :type => :list
if all_tsv.nil?
all_tsv = TSV.setup({}, :key_field => 'Mutation ID', :fields => ["Sample", "Cohort", "Genomic Mutation"] + parser.fields, :type => :list)
end
TSV.traverse parser, :into => all_tsv do |sample, values|
chr, strand, pos, ref, alt, *rest = values
mutation = [chr, pos, alt] * ":"
id = [sample, mutation] * "_"
[id, [sample, cohort, mutation] + values]
end
end
end
end
all_tsv.to_s
end
end
iif Intogen.driver_mutations_catalog.produce.find if __FILE__ == $0
Version data entries
36 entries across 36 versions & 1 rubygems