[BioRuby-cvs] bioruby/lib/bio/shell/plugin flatfile.rb,1.5,1.6

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/lib/bio/shell/plugin
In directory pub.open-bio.org:/tmp/cvs-serv1421/plugin

Modified Files:
	flatfile.rb 
Log Message:
* flatfile method is added (similar to flatauto but returns raw entry)
* save_fasta method is renamed to flatfasta
* parse method is added which parse the entry string to obj by autodetection
* flatindex/flatsearch is changed to ask and uses USERDIR when SAVEDIR
  is not available


Index: flatfile.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/flatfile.rb,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** flatfile.rb	14 Nov 2005 02:01:54 -0000	1.5
--- flatfile.rb	16 Nov 2005 04:01:10 -0000	1.6
***************
*** 33,36 ****
--- 33,53 ----
    private
  
+   def flatfile(filename)
+     if block_given?
+       Bio::FlatFile.auto(filename) do |flat|
+         flat.each do |entry|
+           yield flat.entry_raw
+         end
+       end
+     else
+       entry = ''
+       Bio::FlatFile.auto(filename) do |flat|
+         flat.next_entry
+         entry = flat.entry_raw
+       end
+       return entry
+     end
+   end
+ 
    def flatauto(filename)
      if block_given?
***************
*** 41,52 ****
        end
      else
!       flat = Bio::FlatFile.auto(filename)
!       entry = flat.next_entry
!       flat.close
        return entry
      end
    end
  
!   def save_fasta(fastafile, *flatfiles)
      puts "Saving fasta file (#{fastafile}) ... "
      File.open(fastafile, "w") do |fasta|
--- 58,76 ----
        end
      else
!       entry = ''
!       Bio::FlatFile.auto(filename) do |flat|
!         entry = flat.next_entry
!       end
        return entry
      end
    end
  
!   def parse(entry)
!     if cls = Bio::FlatFile.autodetect(entry)
!       return cls.new(entry)
!     end
!   end
! 
!   def flatfasta(fastafile, *flatfiles)
      puts "Saving fasta file (#{fastafile}) ... "
      File.open(fastafile, "w") do |fasta|
***************
*** 65,80 ****
  
    def flatindex(dbname, *flatfiles)
!     prefix = Core::SAVEDIR + Core::BIOFLAT
!     unless File.directory?(prefix)
!       Bio::Shell.create_save_dir
!     end
!     dir = prefix + dbname.to_s
!     bdb = format = options = nil
      begin
!       print "Creating BioFlat index (#{dir}) ... "
!       Bio::FlatFileIndex.makeindex(bdb, dir, format, options, *flatfiles)
        puts "done"
      rescue
!       raise "Failed to create index (#{dir}) : #{$!}"
      end
    end
--- 89,101 ----
  
    def flatindex(dbname, *flatfiles)
!     prefix = Bio::Shell.create_save_dir + Core::BIOFLAT
!     idxdir = prefix + dbname.to_s
      begin
!       print "Creating BioFlat index (#{idxdir}) ... "
!       bdb = format = options = nil
!       Bio::FlatFileIndex.makeindex(bdb, idxdir, format, options, *flatfiles)
        puts "done"
      rescue
!       raise "Failed to create index (#{idxdir}) : #{$!}"
      end
    end
***************
*** 82,85 ****
--- 103,107 ----
    def flatsearch(dbname, keyword)
      dir = Core::SAVEDIR + Core::BIOFLAT + dbname.to_s
+     dir = Core::USERDIR + Core::BIOFLAT + dbname.to_s unless File.exists?(dir)
      Bio::FlatFileIndex.open(dir) do |db|
        if results = db.include?(keyword)