bio 0.7.0

data/lib/bio/shell/plugin/seq.rb

@@ -0,0 +1,238 @@
+#
+# = bio/shell/plugin/seq.rb - plugin for biological sequence manipulations
+#
+# Copyright::	Copyright (C) 2005
+#		Toshiaki Katayama <k@bioruby.org>
+# License::	LGPL
+#
+# $Id: seq.rb,v 1.16 2005/12/19 01:20:06 k Exp $
+#
+#--
+#
+#  This library is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU Lesser General Public
+#  License as published by the Free Software Foundation; either
+#  version 2 of the License, or (at your option) any later version.
+#
+#  This library is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+#  Lesser General Public License for more details.
+#
+#  You should have received a copy of the GNU Lesser General Public
+#  License along with this library; if not, write to the Free Software
+#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
+#
+#++
+#
+
+module Bio::Shell
+
+  private
+
+  # Convert sequence to colored HTML string
+  def htmlseq(str)
+    if str.kind_of?(Bio::Sequence)
+      seq = str
+    else
+      seq = seq(str)
+    end
+
+    if seq.is_a?(Bio::Sequence::AA)
+      scheme = Bio::ColorScheme::Taylor
+    else
+      scheme = Bio::ColorScheme::Nucleotide
+    end
+
+    html = %Q[<div style="font-family:monospace;">\n]
+    seq.fold(50).each_byte do |c|
+      case c.chr
+      when "\n"
+        html += "<br>\n"
+      else
+        color = scheme[c.chr]
+        html += %Q[<span style="background:\##{color};">#{c.chr}</span>\n]
+      end
+    end
+    html += "</div>\n"
+    return html
+  end
+
+
+  # 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 = seq.subseq(1, max+2).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 << codontable(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"
+    puts rep
+    return rep
+  end
+
+  # Displays a DNA sequence by ascii art in B-type double helix.
+  # Argument need to be at least 16 bases in length.
+  def doublehelix(str)
+    seq = seq(str)
+    if str.length < 16
+      warn "Error: Sequence must be longer than 16 bases."
+      return
+    end
+    if ! seq.respond_to?(:complement)
+      warn "Error: Sequence must be a DNA sequence."
+      return
+    end
+    pairs = [ [5, 0], [4, 2], [3, 3], [2, 4], 
+              [1, 4], [0, 3], [0, 2], [1, 0] ]
+    seq.window_search(16, 16) do |subseq|
+      pairs.each_with_index do |ij, x|
+        base = subseq[x, 1]
+        puts ' ' * ij[0] + base + '-' * ij[1] + base.complement + "\n"
+      end
+      pairs.reverse.each_with_index do |ij, x|
+        base = subseq[x + 8, 1]
+        puts ' ' * ij[0] + base.complement + '-' * ij[1] + base + "\n"
+      end
+    end
+  end
+
+end
+
+
+class String
+
+  def to_naseq
+    Bio::Sequence::NA.new(self)
+  end
+
+  def to_aaseq
+    Bio::Sequence::AA.new(self)
+  end
+
+  # folding both line end justified
+  def fold(fill_column = 72, indent = 0)
+    str = ''
+
+    # size : allowed length of the actual text
+    unless (size = fill_column - indent) > 0
+      warn "Error: indent > fill_column (indent is set to 0)"
+      size = fill_column
+      indent = 0
+    end
+
+    0.step(self.length - 1, size) do |n|
+      str << ' ' * indent + self[n, size] + "\n"
+    end
+
+    return str
+  end
+
+  # folding with conscious about word boundaries with prefix string
+  def fill(fill_column = 80, indent = 0, separater = ' ', prefix = '', first_line_only = true)
+
+    # size : allowed length of the actual text
+    unless (size = fill_column - indent) > 0
+      warn "Error: indent > fill_column (indent is set to 0)"
+      size = fill_column
+      indent = 0
+    end
+
+    n = pos = 0
+    ary = []
+    while n < self.length
+      pos = self[n, size].rindex(separater)
+
+      if self[n, size].length < size	# last line of the folded str
+        pos = nil
+      end
+
+      if pos
+        ary << self[n, pos+separater.length]
+        n += pos + separater.length
+      else				# line too long or the last line
+        ary << self[n, size]
+        n += size
+      end
+    end
+    str = ary.join("\n")
+
+    str[0,0] = prefix + ' ' * (indent - prefix.length)
+    if first_line_only
+      head = ' ' * indent
+    else
+      head = prefix + ' ' * (indent - prefix.length)
+    end
+    str.gsub!("\n", "\n#{head}")
+
+    return str.chomp
+  end
+end
+

data/lib/bio/shell/session.rb

@@ -0,0 +1,214 @@
+#
+# = bio/shell/session.rb - core user interface of the BioRuby shell
+#
+# Copyright::	Copyright (C) 2005
+#		Toshiaki Katayama <k@bioruby.org>
+# License::	LGPL
+#
+# $Id: session.rb,v 1.11 2005/12/07 07:50:44 k Exp $
+#
+#--
+#
+#  This library is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU Lesser General Public
+#  License as published by the Free Software Foundation; either
+#  version 2 of the License, or (at your option) any later version.
+#
+#  This library is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+#  Lesser General Public License for more details.
+#
+#  You should have received a copy of the GNU Lesser General Public
+#  License along with this library; if not, write to the Free Software
+#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
+#
+#++
+#
+
+module Bio::Shell
+
+  private
+
+  ### work space
+
+  def ls
+    list = eval("local_variables", conf.workspace.binding).reject { |x|
+      eval(x, conf.workspace.binding).nil?
+    }
+    puts list.inspect
+  end
+
+  def rm(name)
+    list = eval("local_variables", conf.workspace.binding).reject { |x|
+      eval(x, conf.workspace.binding).nil?
+    }
+    begin
+      if list.include?(name.to_s)
+        eval("#{name} = nil", conf.workspace.binding)
+      else
+        raise
+      end
+    rescue
+      warn "Usage: rm :var or rm 'var' (rm var is not valid)"
+    end
+  end
+
+  ### script
+
+  def script(mode = nil)
+    Bio::Shell.script(mode)
+  end
+
+  ### object
+
+  def reload_object
+    Bio::Shell.load_object
+  end
+
+  ### plugin
+
+  def reload_plugin
+    Bio::Shell.load_plugin
+  end
+
+  ### config
+
+  def config(mode = :show, *opts)
+    case mode
+    when :show, "show"
+      Bio::Shell.config_show
+    when :echo, "echo"
+      Bio::Shell.config_echo
+    when :color, "color"
+      Bio::Shell.config_color
+    when :pager, "pager"
+      Bio::Shell.config_pager(*opts)
+    when :message, "message"
+      Bio::Shell.config_message(*opts)
+    end
+  end
+
+  def reload_config
+    Bio::Shell.load_config
+  end
+
+  ### pager
+
+  def pager(cmd = nil)
+    unless Bio::Shell.config[:pager]
+      cmd = ENV['PAGER'] || cmd
+    end
+    Bio::Shell.config_pager(cmd)
+    puts "Pager is set to '#{cmd ? cmd : 'off'}'"
+  end
+
+  def display(*obj)
+    # The original idea is from http://sheepman.parfait.ne.jp/20050215.html
+    if Bio::Shell.config[:pager]
+      pg = IO.popen(Bio::Shell.config[:pager], "w")
+      begin
+        stdout_save = STDOUT.clone
+        STDOUT.reopen(pg)
+        puts(*obj)
+      ensure
+        STDOUT.reopen(stdout_save)
+        stdout_save.close
+        pg.close
+      end
+    else
+      puts(*obj)
+    end
+  end
+
+  def less(file)
+    pager = Bio::Shell.config[:pager] || ENV['PAGER'] || "less"
+    system("#{pager} #{file}")
+  end
+
+  def head(arg, num = 10)
+    str = ""
+    if File.exists?(arg)
+      File.open(arg) do |file|
+        num.times do
+          if line = file.gets
+            str << line
+          end
+        end
+      end
+    else
+      arg.to_s.each_with_index do |line, i|
+        break if i >= num
+        str << line
+      end
+    end
+    puts str
+    return str
+  end
+
+  ### file save
+
+  def savefile(file, *objs)
+    if File.exists?(file)
+      loop do
+        print "Overwrite existing #{file}? [y/n]: "
+        answer = gets
+        return if /^\s*[Nn]/.match(answer)
+        break if /^\s*[Yy]/.match(answer)
+      end
+    end
+    begin
+      print "Saving data (#{file}) ... "
+      File.open(file, "w") do |f|
+        objs.each do |obj|
+          f.puts obj.to_s
+        end
+      end
+      puts "done"
+    rescue
+      warn "Error: Failed to save (#{file}) : #{$!}"
+    end
+  end
+
+  ### file system
+
+  def cd(dir = ENV['HOME'])
+    if dir
+      Dir.chdir(dir)
+    end
+    puts Dir.pwd.inspect
+  end
+
+  def pwd
+    puts Dir.pwd.inspect
+  end
+
+  def dir(file = nil)
+    if file
+      if File.directory?(file)
+        files = Dir.glob("#{file}/*")
+      else
+        files = Dir.glob(file)
+      end
+    else
+      files = Dir.glob("*")
+    end
+    if files
+      str  = "   UGO  Date                                 Byte  File\n"
+      str << "------  ----------------------------  -----------  ------------\n"
+      files.sort.each { |f|
+        stat = File.lstat(f)
+        mode = format("%6o", stat.mode)
+        date = stat.mtime
+        byte = stat.size
+        name = f.inspect
+        str << format("%s  %s%13d  %s\n", mode, date, byte, name)
+      }
+      puts str
+      return str
+    end
+  end
+
+end
+
+