Sha256: 9a51139ca01f4249c2710278a236396444e0f92ce74327f8c263ed8f740cf331
Contents?: true
Size: 1.09 KB
Versions: 11
Compression:
Stored size: 1.09 KB
Contents
#!/usr/local/bin/ruby-1.9
#
# Usage:: symbol2summary.rb <Gene_Symbol> (default is "TP53")
#
# Copyright::
# Copyright (C) 2011 MISHIMA, Hiroyuki
# <missy at be.to / hmishima at ngit agasaki-u.ac.jp>
# License:: The Ruby licence (Ryby's / GPLv2 dual)
#
#require File.dirname(__FILE__) + '/../lib/bio-ucsc'
require 'bio-ucsc'
require 'nkf'
require 'active_record'
require 'logger'
ActiveRecord::Base.logger = Logger.new("sql.log")
ActiveRecord::Base.logger.level = 0
class Sym2Sum
def run(genesym)
Bio::Ucsc::Hg19::DBConnection.connect
known_gene = Bio::Ucsc::Hg19::KgXref.find_by_geneSymbol(genesym)
ref_gene = Bio::Ucsc::Hg19::RefGene.find_by_name2(genesym)
summary = Bio::Ucsc::Hg19::RefSeqSummary.find_by_mrnaAcc(ref_gene.name).summary
puts "---"
puts "Gene symbol: #{genesym}" if known_gene
puts "Description: #{known_gene.description}" if known_gene
if summary
puts "Summary:"
puts NKF.nkf("-wF72", summary)
end
end
end
if $0 == __FILE__
genesym = ARGV[0]
genesym ||= "TP53"
Sym2Sum.new.run(genesym)
end
Version data entries
11 entries across 11 versions & 1 rubygems