Sha256: 4ed64133389a82da01880b9424b3a067718ceabf4616c30fae44e8cc0155269d
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Versions: 364
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Stored size: 1.44 KB
Contents
#!/usr/bin/env ruby
require 'rbbt-util'
require 'rbbt/util/simpleopt'
require 'rbbt/sources/organism'
options = SOPT.get("-i--identifiers*:-f--format*:-o--organism*:-p--persistence:-l--log*:-r--report:-h--hash")
file = ARGV[0]
if not File.exists? file
base, path = file.match(/([^.]*)\.(.*)/).values_at 1, 2
require 'rbbt/sources/' << base.to_s.downcase
klass = Misc.string2const base
file = klass[path].find
end
entities = ARGV[1].nil? ? '-' : ARGV[1].dup
persistence = options[:persistence]
log = (options[:log] || 4).to_i
Log.severity = log
organism = options[:organism] || "Hsa"
identifiers = options[:identifiers] || Organism.identifiers(organism)
format = options[:format]
report = options[:report]
if format.to_s == "key"
File.open(file) do |f|
format = TSV.parse_header(f).first
end
end
if format.nil?
f, count = TSV.new(identifiers).guess_field(entities)
format = f if count > 0
end
data = if entities == '-'
TSV.new(STDIN)
#entities = TSV.new(STDIN.read.split(/\n|\||\t/)
else
entities = [entities]
data = TSV.new(entities)
data.type = :double
data.identifiers = identifiers
data.key_field = format.dup unless FalseClass === format or format.nil?
data.fields ||= []
data
end
data.type = :double
data.identifiers = identifiers
data.attach TSV.new file, :persistence => persistence
if report
data.each do |entity,values|
puts "== Entity: #{ entity }"
puts values.report
end
else
puts data
end
Version data entries
364 entries across 364 versions & 1 rubygems