[BioRuby-cvs] bioruby/lib/bio/db/embl format_embl.rb, 1.1.2.4, 1.1.2.5

[Naohisa Goto]

Update of /home/repository/bioruby/bioruby/lib/bio/db/embl
In directory dev.open-bio.org:/tmp/cvs-serv13173/lib/bio/db/embl

Modified Files:
      Tag: BRANCH-biohackathon2008
	format_embl.rb 
Log Message:
simplify code of seq_format_embl(), and SQ line is changed not to show
non-ACGT single base contents (which should be shown together as "other").


Index: format_embl.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/db/embl/Attic/format_embl.rb,v
retrieving revision 1.1.2.4
retrieving revision 1.1.2.5
diff -C2 -d -r1.1.2.4 -r1.1.2.5
*** format_embl.rb	7 May 2008 12:24:26 -0000	1.1.2.4
--- format_embl.rb	28 May 2008 13:38:07 -0000	1.1.2.5
***************
*** 106,121 ****
  
      def seq_format_embl(seq)
-       output_lines = Array.new
        counter = 0
!       remainder = seq.window_search(60,60) do |subseq|
!         counter += 60
!         subseq.gsub!(/(.{10})/, '\1 ')
!         output_lines.push(' '*5 + subseq + counter.to_s.rjust(9))
        end
!       counter += remainder.length
!       remainder = (remainder.to_s + ' '*(60-remainder.length))
!       remainder.gsub!(/(.{10})/, '\1 ')
!       output_lines.push(' '*5 + remainder + counter.to_s.rjust(9))
!       return output_lines.join("\n")
      end
  
--- 106,126 ----
  
      def seq_format_embl(seq)
        counter = 0
!       result = seq.gsub(/.{1,60}/) do |x|
!         counter += x.length
!         x = x.gsub(/.{10}/, '\0 ')
!         sprintf("     %-66s%9d\n", x, counter)
        end
!       result.chomp!
!       result
!     end
! 
!     def seq_composition(seq)
!       { :a => seq.count('aA'),
!         :c => seq.count('cC'),
!         :g => seq.count('gG'),
!         :t => seq.count('tTuU'),
!         :other => seq.count('^aAcCgGtTuU')
!       }
      end
  
***************
*** 140,144 ****
  FH   
  <%= format_features_embl(features || []) %>XX   
! SQ   Sequence <%= seq.length %> BP; <%= seq.composition.collect{|k,v| "#{v} #{k.upcase}"}.join('; ') + '; ' + (seq.gsub(/[ACTGactg]/, '').length.to_s ) + ' other;' %>
  <%= seq_format_embl(seq) %>
  //
--- 145,149 ----
  FH   
  <%= format_features_embl(features || []) %>XX   
! SQ   Sequence <%= seq.length %> BP; <% c = seq_composition(seq) %><%= c[:a] %> A; <%= c[:c] %> C; <%= c[:g] %> G; <%= c[:t] %> T; <%= c[:other] %> other;
  <%= seq_format_embl(seq) %>
  //