[BioRuby-cvs] bioruby/lib/bio/shell/plugin keggapi.rb,1.3,1.4

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/lib/bio/shell/plugin
In directory pub.open-bio.org:/tmp/cvs-serv24669/lib/bio/shell/plugin

Modified Files:
	keggapi.rb 
Log Message:
* some listing methods (orgs, pathways, dbs) are added
* @keggapi is changed to be accessed as keggapi


Index: keggapi.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/keggapi.rb,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** keggapi.rb	14 Nov 2005 02:01:54 -0000	1.3
--- keggapi.rb	25 Nov 2005 16:07:55 -0000	1.4
***************
*** 33,45 ****
    private
  
!   def setup_keggapi
      unless @keggapi
        @keggapi = Bio::KEGG::API.new
      end
    end
  
    def bfind(str)
!     setup_keggapi
!     result = @keggapi.bfind(str)
      display result
      return result
--- 33,61 ----
    private
  
!   def keggapi
      unless @keggapi
        @keggapi = Bio::KEGG::API.new
      end
+     return @keggapi
+   end
+ 
+   def _definition(list)
+     ary = []
+     list.each do |entry|
+       ary << "#{entry.entry_id}:\t#{entry.definition}"
+     end
+     return ary
+   end
+ 
+   # DBGET
+ 
+   def binfo(db = "all")
+     result = keggapi.binfo(db)
+     display result
+     return result
    end
  
    def bfind(str)
!     result = keggapi.bfind(str)
      display result
      return result
***************
*** 47,70 ****
  
    def bget(str)
!     setup_keggapi
!     entry = @keggapi.bget(str)
      if block_given?
!       yield entry
      else
!       display entry
      end
!     return entry
    end
  
  end
  
  =begin
- --- list_databases
- --- list_organisms
- --- list_pathways(org)
- --- binfo(string)
- --- bfind(string)
- --- bget(string)
- --- btit(string)
  --- get_linkdb_by_entry(entry_id, db, start, max_results)
  --- get_best_best_neighbors_by_gene(genes_id, start, max_results)
--- 63,136 ----
  
    def bget(str)
!     result = keggapi.bget(str)
      if block_given?
!       yield result
      else
!       display result
      end
!     return result
!   end
! 
!   def btit(str)
!     result = keggapi.btit(str)
!     display result
!     return result
!   end
! 
!   def bconv(str)
!     result = keggapi.bconv(str)
!     display result
!     return result
!   end
! 
!   # DATABASES
! 
!   def keggdbs
!     list = keggapi.list_databases
!     result = _definition(list).join("\n")
!     display result
!     return result
!   end
! 
!   def keggorgs
!     list = keggapi.list_organisms
!     result = _definition(list).sort.join("\n")
!     display result
!     return result
!   end
! 
!   def keggpathways(org = "map")
!     list = keggapi.list_pathways(org)
!     result = _definition(list).join("\n")
!     display result
!     return result
!   end
! 
!   #--
!   # *TODO* use kegg das instead?
!   #++
!   def kegggenome(org)
!     result = ""
!     require 'net/ftp'
!     Net::FTP.open("ftp.genome.jp", "anonymous") do |ftp|
!       path = "/pub/kegg/genomes/#{org}"
!       list = ftp.nlst(path)
!       file = list.grep(/.*genome$/).shift
!       if file
!         base = File.basename(file)
!         ftp.getbinaryfile(file, base)
!         result = File.read(base)
!       end
!     end
!     return result
    end
  
+ # def kegggene(genes_id)
+ #    keggapi.bget()
+ # end
+ 
  end
  
  =begin
  --- get_linkdb_by_entry(entry_id, db, start, max_results)
  --- get_best_best_neighbors_by_gene(genes_id, start, max_results)