lib/bio/db/go.rb in bio-1.3.1 vs lib/bio/db/go.rb in bio-1.4.0

@@ -3,11 +3,11 @@
 #
 # Copyright::   Copyright (C) 2003 
 #               Mitsuteru C. Nakao <[e-mail]>
 # License::     The Ruby License
 #
-#  $Id: go.rb,v 1.11 2007/04/05 23:35:40 trevor Exp $
+#  $Id:$
 #
 # == Gene Ontology
 #
 # == Example
 #
@@ -87,11 +87,11 @@
     # constructing adjaency list for the given ontology
     def dag_edit_format_parser(str)
       stack    = []
       adj_list = []
       
-      str.each {|line|
+      str.each_line {|line|
         if /^!(.+?):\s+(\S.+)$/ =~ line  # Parsing head lines
           tag   = $1
           value = $2
           tag.gsub!(/-/,'_')
           next if tag == 'type'
@@ -196,17 +196,17 @@
 
     # Retruns an Array of parsed gene_association flatfile.
     # Block is acceptable.  
     def self.parser(str)
       if block_given?
-        str.each(DELIMITER) {|line|
+        str.each_line(DELIMITER) {|line|
           next if /^!/ =~ line
           yield GeneAssociation.new(line)
         }
       else
         galist = []
-        str.each(DELIMITER) {|line|
+        str.each_line(DELIMITER) {|line|
           next if /^!/ =~ line
           galist << GeneAssociation.new(line)
         }
         return galist
       end
@@ -409,73 +409,5 @@
 
 
 
 
 
-if __FILE__ == $0
-
-  require 'net/http'
-
-  def wget(url)
-    if /http:\/\/(.+?)\// =~ url
-      host = $1
-      path = url[(url.index(host) + host.size)..url.size]
-    else
-      raise ArgumentError, "Invalid URL\n#{url}"
-    end
-
-    result = Net::HTTP.new(host).get(path).body
-  end
-
-
-
-  go_c_url = 'http://www.geneontology.org/ontology/component.ontology'
-  ga_url = 'http://www.geneontology.org/gene-associations/gene_association.sgd.gz'
-  e2g_url = 'http://www.geneontology.org/external2go/spkw2go'
-
-
-
-  puts "\n #==> Bio::GO::Ontology"
-  p go_c_url
-  component_ontology = wget(go_c_url)
-  comp = Bio::GO::Ontology.new(component_ontology)
-
-  [['0003673', '0005632'],
-    ['0003673', '0005619'],
-    ['0003673', '0004649']].each {|pair|
-    puts
-    p pair
-    p [:pair, pair.map {|i| [comp.id2term[i], comp.goid2term(i)] }]
-    puts "\n #==> comp.bfs_shortest_path(pair[0], pair[1])"
-    p comp.bfs_shortest_path(pair[0], pair[1])
-  }
-
-
-  puts "\n #==> Bio::GO::External2go"
-  p e2g_url
-  spkw2go = Bio::GO::External2go.new(wget(e2g_url))
-
-  puts "\n #==> spkw2go.db"
-  p spkw2go.db
-
-  puts "\n #==> spkw2go[1]"
-  p spkw2go[1]
-
-
-
-  require 'zlib'
-  puts "\n #==> Bio::GO::GeenAssociation"
-  p ga_url
-  ga = Zlib::Inflate.inflate(wget(ga_url))
-  ga = Bio::GO::GeneAssociation.parser(ga)
-
-  puts "\n #==> ga.size"
-  p ga.size
-
-  puts "\n #==> ga[100]"
-  p ga[100]
-
-
-
-
-  
-end