Class: Bio::GGGenome

Inherits:
Object
  • Object
show all
Defined in:
lib/bio-gggenome/gggenome.rb

Overview

Bio::GGGenome

gggenome = Bio::GGGenome.new hits = gggenome.search(“hg19”, 1, “TTCATTGACAACATT”) hits = gggenome.search(“hg19”, “TTCATTGACAACATT”) hits = gggenome.search(“TTCATTGACAACATT”)

hits = Bio::GGGenome.search(“hg19”, “TTCATTGACAACATT”)

Constant Summary collapse

BASE_URL = 
"http://gggenome.dbcls.jp"

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(uri = BASE_URL) ⇒ GGGenome

Returns a new instance of GGGenome.



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# File 'lib/bio-gggenome/gggenome.rb', line 24

def initialize(uri = BASE_URL)
  uri = URI.parse(uri) unless uri.kind_of?(URI)
  @pathbase = uri.path
  @pathbase = '/' + @pathbase unless /\A\// =~ @pathbase
  @pathbase = @pathbase + '/' unless /\/\z/ =~ @pathbase
  @http = Bio::Command.new_http(uri.host, uri.port)
  @header = {
    'User-Agent' => "BioRuby/#{Bio::BIORUBY_VERSION_ID}"
  }
end

Class Method Details

.search(*args) ⇒ Object 



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# File 'lib/bio-gggenome/gggenome.rb', line 20

def self.search(*args)
  new.search(args)
end

Instance Method Details

#search(*args) ⇒ Object

Search, returns a result hash. Bio::GGGenome#search(“hg19”, 1, “TTCATTGACAACATT”) Bio::GGGenome#search(“hg19”, “TTCATTGACAACATT”) Bio::GGGenome#search(1, “TTCATTGACAACATT”) Bio::GGGenome#search(“TTCATTGACAACATT”) Bio::GGGenome#search(“gggenome.dbcls.jp/hg19/TTCATTGACAACATTGCGT.json”)



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# File 'lib/bio-gggenome/gggenome.rb', line 41

def search(*args)
  db        = nil
  missmatch = nil
  
  if args[0] =~ /^http/
    args[0].sub!(BASE_URL, '')
    args[0].sub!(/^\//,'')
    args[0].sub!(".json", '')
    args = args[0].split("/")        
  end
  
  case args.size
  when 1
    seq = args.shift
  when 2
    if args[0].to_s.strip =~ /^[0-9]+$/
      missmatch,seq = args
    else
      db,seq = args
    end  
  when 3
    db,missmatch,seq = args
  else
    raise ArgumentError
  end     
  query = ['', db, missmatch, seq].compact.join("/")
  path =  query + ".json"
  begin
    response = @http.get(path, @header)
  rescue
  end

  case response.code
  when "200"
    JSON.parse(response.body)
  when "302"
    location = response.header['Location']
    search(location)
  else
    nil
  end
end