[BioRuby-cvs] bioruby/lib/bio/shell/plugin seq.rb,1.10,1.11

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/lib/bio/shell/plugin
In directory pub.open-bio.org:/tmp/cvs-serv24566/lib/bio/shell/plugin

Modified Files:
	seq.rb 
Log Message:
* seqstat method improved
  * truncate long sequence to display
  * compositions are pretty printed with percentage with names
  * codon usage is now displayed in the codon table (also in color mode)


Index: seq.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/shell/plugin/seq.rb,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** seq.rb	24 Nov 2005 19:32:04 -0000	1.10
--- seq.rb	25 Nov 2005 16:05:41 -0000	1.11
***************
*** 29,32 ****
--- 29,33 ----
  require 'bio/sequence'
  require 'bio/util/color_scheme'
+ require 'bio/shell/plugin/codon'
  
  module Bio::Shell
***************
*** 99,140 ****
    # Displays some basic properties of the sequence.
    def seqstat(str)
      seq = seq(str)
!     rep = ""
      if seq.respond_to?(:complement)
!       rep << "Sequence           : #{seq.fold(71,21).strip}\n"
!       rep << "Reverse complement : #{seq.complement.fold(71,21).strip}\n"
!       rep << "Translation  1     : #{seq.translate.fold(71,21).strip}\n"
!       rep << "Translation  2     : #{seq.translate(2).fold(71,21).strip}\n"
!       rep << "Translation  3     : #{seq.translate(3).fold(71,21).strip}\n"
!       rep << "Translation -1     : #{seq.translate(-1).fold(71,21).strip}\n"
!       rep << "Translation -2     : #{seq.translate(-2).fold(71,21).strip}\n"
!       rep << "Translation -3     : #{seq.translate(-3).fold(71,21).strip}\n"
!       rep << "GC percent         : #{seq.gc_percent} %\n"
!       rep << "Composition        : #{seq.composition.inspect}\n"
!       begin
!         rep << "Molecular weight   : #{seq.molecular_weight}\n"
!       rescue
!         rep << "Molecular weight   : #{$!}\n"
        end
        begin
!         rep << "Complemnet weight  : #{seq.complement.molecular_weight}\n"
        rescue
!         rep << "Complement weight  : #{$!}\n"
        end
        begin
!         rep << "Protein weight     : #{seq.translate.molecular_weight}\n"
        rescue
!         rep << "Protein weight     : #{$!}\n"
        end
      else
!       rep << "Sequence           : #{seq.fold(71,21).strip}\n"
!       rep << "Composition        : #{seq.composition.inspect}\n"
        begin
!         rep << "Protein weight     : #{seq.molecular_weight}\n"
        rescue
!         rep << "Protein weight     : #{$!}\n"
        end
- #     rep << "amino acid codes   : #{seq.codes.inspect}\n"
- #     rep << "amino acid names   : #{seq.names.inspect}\n"
      end
      rep  << "//\n"
--- 100,174 ----
    # Displays some basic properties of the sequence.
    def seqstat(str)
+     max = 150
      seq = seq(str)
!     rep = "\n* * * Sequence statistics * * *\n\n"
      if seq.respond_to?(:complement)
!       fwd = seq
!       rev = seq.complement
!       if seq.length > max
!         dot = " ..."
!         fwd = fwd.subseq(1, max)
!         rev = rev.subseq(1, max)
!       end
!       rep << "5'->3' sequence   : #{fwd.fold(70,20).strip}#{dot}\n"
!       rep << "3'->5' sequence   : #{rev.fold(70,20).strip}#{dot}\n"
!       [ 1, 2, 3, -1, -2, -3 ].each do |frame|
!         pep = fwd.translate(frame).fold(70,20).strip
!         rep << "Translation  #{frame.to_s.rjust(2)}   : #{pep}#{dot}\n"
!       end
!       rep << "Length            : #{seq.length} bp\n"
!       rep << "GC percent        : #{seq.gc_percent} %\n"
! 
!       ary = []
!       seq.composition.sort.each do |base, num|
!         percent = format("%.2f", 100.0 * num / seq.length).rjust(6)
!         count   = num.to_s.rjust(seq.length.to_s.length)
!         ary << "                    #{base} - #{count} (#{percent} %)\n"
!       end
!       rep << "Composition       : #{ary.join.strip}\n"
! 
!       rep << "Codon usage       :\n"
!       hash = Hash.new("0.0%")
!       seq.codon_usage.sort.each do |codon, num|
!         percent = format("%.1f%", 100.0 * num / (seq.length / 3))
!         hash[codon] = percent
        end
+       rep << codon_usage_table(1, hash).output
+ 
        begin
!         rep << "Molecular weight  : #{seq.molecular_weight}\n"
        rescue
!         rep << "Molecular weight  : #{$!}\n"
        end
        begin
!         rep << "Protein weight    : #{seq.translate.chomp('*').molecular_weight}\n"
        rescue
!         rep << "Protein weight    : #{$!}\n"
        end
      else
!       pep = seq
!       if seq.length > max
!         dot = " ..."
!         pep = seq.subseq(1, max)
!       end
!       rep << "N->C sequence     : #{pep.fold(70,20).strip}#{dot}\n"
!       rep << "Length            : #{seq.length} aa\n"
! 
!       names = Bio::AminoAcid.names
!       ary = []
!       seq.composition.sort.each do |aa, num|
!         percent = format("%.2f", 100.0 * num / seq.length).rjust(6)
!         count   = num.to_s.rjust(seq.length.to_s.length)
!         code    = names[aa]
!         name    = names[names[aa]]
!         ary << "                    #{aa} #{code} - #{count} (#{percent} %) #{name}\n"
!       end
!       rep << "Composition       : #{ary.join.strip}\n"
! 
        begin
!         rep << "Protein weight    : #{seq.molecular_weight}\n"
        rescue
!         rep << "Protein weight    : #{$!}\n"
        end
      end
      rep  << "//\n"