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Contents
require 'rbbt'
module EBChromatin
BASE_URL='http://hgdownload-test.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeBroadHmm/'
TISSUES= %w(Gm12878 H1hesc Hmec Hsmm Huvec Hepg2 K562 Nhek Nhlf)
TISSUES.each do |tissue|
file = "wgEncodeBroadHmm#{tissue}HMM.bed.gz"
Rbbt.claim Rbbt.share.databases.EBChromatin[file.match(/wgEncodeBroadHmm(.*)HMM.bed.gz/)[1]], :proc do
url = File.join(BASE_URL, file)
CMD.cmd('sed \'s/^chr\([[:alnum:]]\+\)\t\([[:digit:]]\+\)\t\([[:digit:]]\+\)/\1:\2:\3\t\1\t\2\t\3/\' | cut -f 1,2,3,4,5 | awk \'BEGIN {print "#Region ID\tChromosome Name\tStart\tEnd\tType"} /./ {print $0}\' ', :in => Open.read(url), :pipe => true).read
end
end
def self.chromosome(tissue, chr, positions)
list = Array === positions ? positions : [positions]
file = Rbbt.share.databases.EBChromatin[tissue]
chromosome_bed = Persistence.persist(file, "EBChromatin[#{tissue}][#{chr}]", :fwt, :chromosome => chr, :range => true) do |file, options|
chromosome = options[:chromosome]
tsv = file.tsv(:persist => false, :type => :list, :grep => "^#{chromosome}:\\|^#")
if tsv.size > 0
tsv.collect do |gene, values|
[gene, values.values_at("Start", "End").collect{|p| p.to_i}]
end
else
raise "No chromatin information for chromosome #{ chr } in tissue #{ tissue }"
end
end
list.collect do |pos| chromosome_bed[pos] end
end
end
Version data entries
116 entries across 116 versions & 1 rubygems