bio 0.7.0

data/lib/bio/command.rb

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+#
+# = bio/command.rb - general methods for external command execution
+#
+# Copyright::	Copyright (C) 2003-2005
+# 		Naohisa Goto <ng@bioruby.org>,
+#		Toshiaki Katayama <k@bioruby.org>
+# License::	LGPL
+#
+#  $Id: command.rb,v 1.3 2005/11/04 17:36:00 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
+#
+#++
+#
+
+require 'open3'
+
+module Bio
+module Command
+
+# = Bio::Command::Tools
+#
+# Bio::Command::Tools is a collection of useful methods for execution
+# of external commands or web applications. Any wrapper class for
+# applications shall include this class. Note that all methods below
+# are private except for some methods.
+module Tools
+
+  UNSAFE_CHARS_UNIX   = /[^A-Za-z0-9\_\-\.\:\,\/\@\x1b\x80-\xfe]/n
+  QUOTE_CHARS_WINDOWS = /[^A-Za-z0-9\_\-\.\:\,\/\@\\]/n
+  UNESCAPABLE_CHARS   = /[\x00-\x08\x10-\x1a\x1c-\x1f\x7f\xff]/n
+
+  #module_function
+  private
+
+  # Escape special characters in command line string for cmd.exe on Windows.
+  def escape_shell_windows(str)
+    str = str.to_s
+    raise 'cannot escape control characters' if UNESCAPABLE_CHARS =~ str
+    if QUOTE_CHARS_WINDOWS =~ str then
+      '"' + str.gsub(/\"/, '""') + '"'
+    else
+      String.new(str)
+    end
+  end
+
+  # Escape special characters in command line string for UNIX shells.
+  def escape_shell_unix(str)
+    str = str.to_s
+    raise 'cannot escape control characters' if UNESCAPABLE_CHARS =~ str
+    str.gsub(UNSAFE_CHARS_UNIX) { |x| "\\#{x}" }
+  end
+
+  # Escape special characters in command line string.
+  def escape_shell(str)
+    case RUBY_PLATFORM
+    when /mswin32|bccwin32/
+      escape_shell_windows(str)
+    else
+      escape_shell_unix(str)
+    end
+  end
+
+  # Generate command line string with special characters escaped.
+  def make_command_line(ary)
+    case RUBY_PLATFORM
+    when /mswin32|bccwin32/
+      make_command_line_windows(ary)
+    else
+      make_command_line_unix(ary)
+    end
+  end
+
+  # Generate command line string with special characters escaped
+  # for cmd.exe on Windows.
+  def make_command_line_windows(ary)
+    ary.collect { |str| escape_shell_windows(str) }.join(" ")
+  end
+
+  # Generate command line string with special characters escaped
+  # for UNIX shells.
+  def make_command_line_unix(ary)
+    ary.collect { |str| escape_shell_unix(str) }.join(" ")
+  end
+
+  # Executes the program.  Automatically select popen for Windows
+  # environment and open3 for the others.
+  #
+  # If block is given, yield the block with input and output IO objects.
+  # Note that in some platform, inn and out are the same object.
+  # Please be careful to do inn.close and out.close.
+  def call_command_local(cmd, query = nil, &block)
+    case RUBY_PLATFORM
+    when /mswin32|bccwin32/
+      call_command_local_popen(cmd, query, &block)
+    else
+      call_command_local_open3(cmd, query, &block)
+    end
+  end
+
+  # Executes the program via IO.popen for OS which doesn't support fork.
+  # If block is given, yield the block with IO objects.
+  # The two objects are the same because of limitation of IO.popen.
+  def call_command_local_popen(cmd, query = nil)
+    str = make_command_line(cmd)
+    IO.popen(str, "w+") do |io|
+      if block_given? then
+        io.sync = true
+        yield io, io
+      else
+        io.sync = true
+        io.print query if query
+        io.close_write
+        io.read
+      end
+    end
+  end
+
+  # Executes the program via Open3.popen3
+  # If block is given, yield the block with input and output IO objects.
+  #
+  # From the view point of security, this method is recommended
+  # rather than exec_local_popen.
+  def call_command_local_open3(cmd, query = nil)
+    cmd = cmd.collect { |x| x.to_s }
+    Open3.popen3(*cmd) do |pin, pout, perr|
+      perr.sync = true
+      t = Thread.start { @errorlog = perr.read }
+      if block_given? then
+        yield pin, pout
+      else
+        begin
+          pin.print query if query
+          pin.close
+          output = pout.read
+        ensure
+          t.join
+        end
+        output
+      end
+    end
+  end
+
+  # Shows the latest stderr of the program execution.
+  # Note that this method may be thread unsafe.
+  attr_reader :errorlog
+  public :errorlog
+
+end # module Tools
+end # module Command
+end # module Bio
+

data/lib/bio/data/aa.rb

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+#
+# = bio/data/aa.rb - Amino Acids
+#
+# Copyright::	Copyright (C) 2001, 2005
+#		Toshiaki Katayama <k@bioruby.org>
+# License::	LGPL
+#
+# $Id: aa.rb,v 0.16 2005/11/15 13:33:11 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
+
+class AminoAcid
+
+  module Data
+
+    # IUPAC code
+    # * http://www.iupac.org/
+    # * http://www.chem.qmw.ac.uk/iubmb/newsletter/1999/item3.html
+
+    NAMES = {
+
+      'A' => 'Ala',
+      'C' => 'Cys',
+      'D' => 'Asp',
+      'E' => 'Glu',
+      'F' => 'Phe',
+      'G' => 'Gly',
+      'H' => 'His',
+      'I' => 'Ile',
+      'K' => 'Lys',
+      'L' => 'Leu',
+      'M' => 'Met',
+      'N' => 'Asn',
+      'P' => 'Pro',
+      'Q' => 'Gln',
+      'R' => 'Arg',
+      'S' => 'Ser',
+      'T' => 'Thr',
+      'V' => 'Val',
+      'W' => 'Trp',
+      'Y' => 'Tyr',
+      'B' => 'Asx',	# D/N
+      'Z' => 'Glx',	# E/Q
+      'U' => 'Sec',	# 'uga' (stop)
+      '?' => 'Pyl',	# 'uag' (stop)
+     
+      'Ala' => 'alanine',
+      'Cys' => 'cysteine',
+      'Asp' => 'aspartic acid',
+      'Glu' => 'glutamic acid',
+      'Phe' => 'phenylalanine',
+      'Gly' => 'glycine',
+      'His' => 'histidine',
+      'Ile' => 'isoleucine',
+      'Lys' => 'lysine',
+      'Leu' => 'leucine',
+      'Met' => 'methionine',
+      'Asn' => 'asparagine',
+      'Pro' => 'proline',
+      'Gln' => 'glutamine',
+      'Arg' => 'arginine',
+      'Ser' => 'serine',
+      'Thr' => 'threonine',
+      'Val' => 'valine',
+      'Trp' => 'tryptophan',
+      'Tyr' => 'tyrosine',
+      'Asx' => 'asparagine/aspartic acid',
+      'Glx' => 'glutamine/glutamic acid',
+      'Sec' => 'selenocysteine',
+      'Pyl' => 'pyrrolysine',
+
+    }
+
+    # AAindex FASG760101 - Molecular weight (Fasman, 1976)
+    #   Fasman, G.D., ed.
+    #   Handbook of Biochemistry and Molecular Biology", 3rd ed.,
+    #   Proteins - Volume 1, CRC Press, Cleveland (1976)
+
+    WEIGHT = {
+
+      'A' => 89.09,
+      'C' => 121.15,	# 121.16 according to the Wikipedia
+      'D' => 133.10,
+      'E' => 147.13,
+      'F' => 165.19,
+      'G' => 75.07,
+      'H' => 155.16,
+      'I' => 131.17,
+      'K' => 146.19,
+      'L' => 131.17,
+      'M' => 149.21,
+      'N' => 132.12,
+      'P' => 115.13,
+      'Q' => 146.15,
+      'R' => 174.20,
+      'S' => 105.09,
+      'T' => 119.12,
+      'U' => 168.06,
+      'V' => 117.15,
+      'W' => 204.23,
+      'Y' => 181.19,
+    }
+
+    def weight(x = nil)
+      if x
+        if x.length > 1
+          total = 0.0
+          x.each_byte do |byte|
+            aa = byte.chr.upcase
+            if WEIGHT[aa]
+              total += WEIGHT[aa]
+            else
+              raise "Error: invalid amino acid '#{aa}'"
+            end
+          end
+          total -= NucleicAcid.weight[:water] * (x.length - 1)
+        else
+          WEIGHT[x]
+        end
+      else
+        WEIGHT
+      end
+    end
+
+    def [](x)
+      NAMES[x]
+    end
+
+    # backward compatibility
+    def names
+      NAMES
+    end
+    alias aa names
+
+    def name(x)
+      str = NAMES[x]
+      if str and str.length == 3
+        NAMES[str]
+      else
+        str
+      end
+    end
+
+    def to_1(x)
+      case x.to_s.length
+      when 1
+        x
+      when 3
+        three2one(x)
+      else
+        name2one(x)
+      end
+    end
+    alias one to_1
+
+    def to_3(x)
+      case x.to_s.length
+      when 1
+        one2three(x)
+      when 3
+        x
+      else
+        name2three(x)
+      end
+    end
+    alias three to_3
+
+    def one2three(x)
+      if x and x.length != 1
+        raise ArgumentError
+      else
+        NAMES[x]
+      end
+    end
+
+    def three2one(x)
+      if x and x.length != 3
+        raise ArgumentError
+      else
+        reverse[x]
+      end
+    end
+
+    def one2name(x)
+      if x and x.length != 1
+        raise ArgumentError
+      else
+        three2name(NAMES[x])
+      end
+    end
+
+    def name2one(x)
+      str = reverse[x.to_s.downcase]
+      if str and str.length == 3
+        three2one(str)
+      else
+        str
+      end
+    end
+
+    def three2name(x)
+      if x and x.length != 3
+        raise ArgumentError
+      else
+        NAMES[x]
+      end
+    end
+
+    def name2three(x)
+      reverse[x.downcase]
+    end
+
+    def to_re(seq)
+      str = seq.to_s.upcase
+      str.gsub!(/[^BZACDEFGHIKLMNPQRSTVWYU]/, ".")
+      str.gsub!("B", "[DN]")
+      str.gsub!("Z", "[EQ]")
+      Regexp.new(str)
+    end
+
+
+    private
+
+
+    def reverse
+      hash = Hash.new
+      NAMES.each do |k, v|
+        hash[v] = k
+      end
+      hash
+    end
+
+  end
+
+
+  # as instance methods
+  include Data
+
+  # as class methods
+  extend Data
+
+
+  private
+
+
+  # override when used as an instance method to improve performance
+  alias orig_reverse reverse
+  def reverse
+    unless @reverse
+      @reverse = orig_reverse
+    end
+    @reverse
+  end
+
+end
+
+end # module Bio
+
+
+if __FILE__ == $0
+
+  puts "### aa = Bio::AminoAcid.new"
+  aa = Bio::AminoAcid.new
+
+  puts "# Bio::AminoAcid['A']"
+  p Bio::AminoAcid['A']
+  puts "# aa['A']"
+  p aa['A']
+
+  puts "# Bio::AminoAcid.name('A'), Bio::AminoAcid.name('Ala')"
+  p Bio::AminoAcid.name('A'), Bio::AminoAcid.name('Ala')
+  puts "# aa.name('A'), aa.name('Ala')"
+  p aa.name('A'), aa.name('Ala')
+
+  puts "# Bio::AminoAcid.to_1('alanine'), Bio::AminoAcid.one('alanine')"
+  p Bio::AminoAcid.to_1('alanine'), Bio::AminoAcid.one('alanine')
+  puts "# aa.to_1('alanine'), aa.one('alanine')"
+  p aa.to_1('alanine'), aa.one('alanine')
+  puts "# Bio::AminoAcid.to_1('Ala'), Bio::AminoAcid.one('Ala')"
+  p Bio::AminoAcid.to_1('Ala'), Bio::AminoAcid.one('Ala')
+  puts "# aa.to_1('Ala'), aa.one('Ala')"
+  p aa.to_1('Ala'), aa.one('Ala')
+  puts "# Bio::AminoAcid.to_1('A'), Bio::AminoAcid.one('A')"
+  p Bio::AminoAcid.to_1('A'), Bio::AminoAcid.one('A')
+  puts "# aa.to_1('A'), aa.one('A')"
+  p aa.to_1('A'), aa.one('A')
+
+  puts "# Bio::AminoAcid.to_3('alanine'), Bio::AminoAcid.three('alanine')"
+  p Bio::AminoAcid.to_3('alanine'), Bio::AminoAcid.three('alanine')
+  puts "# aa.to_3('alanine'), aa.three('alanine')"
+  p aa.to_3('alanine'), aa.three('alanine')
+  puts "# Bio::AminoAcid.to_3('Ala'), Bio::AminoAcid.three('Ala')"
+  p Bio::AminoAcid.to_3('Ala'), Bio::AminoAcid.three('Ala')
+  puts "# aa.to_3('Ala'), aa.three('Ala')"
+  p aa.to_3('Ala'), aa.three('Ala')
+  puts "# Bio::AminoAcid.to_3('A'), Bio::AminoAcid.three('A')"
+  p Bio::AminoAcid.to_3('A'), Bio::AminoAcid.three('A')
+  puts "# aa.to_3('A'), aa.three('A')"
+  p aa.to_3('A'), aa.three('A')
+
+  puts "# Bio::AminoAcid.one2three('A')"
+  p Bio::AminoAcid.one2three('A')
+  puts "# aa.one2three('A')"
+  p aa.one2three('A')
+
+  puts "# Bio::AminoAcid.three2one('Ala')"
+  p Bio::AminoAcid.three2one('Ala')
+  puts "# aa.three2one('Ala')"
+  p aa.three2one('Ala')
+
+  puts "# Bio::AminoAcid.one2name('A')"
+  p Bio::AminoAcid.one2name('A')
+  puts "# aa.one2name('A')"
+  p aa.one2name('A')
+
+  puts "# Bio::AminoAcid.name2one('alanine')"
+  p Bio::AminoAcid.name2one('alanine')
+  puts "# aa.name2one('alanine')"
+  p aa.name2one('alanine')
+
+  puts "# Bio::AminoAcid.three2name('Ala')"
+  p Bio::AminoAcid.three2name('Ala')
+  puts "# aa.three2name('Ala')"
+  p aa.three2name('Ala')
+
+  puts "# Bio::AminoAcid.name2three('alanine')"
+  p Bio::AminoAcid.name2three('alanine')
+  puts "# aa.name2three('alanine')"
+  p aa.name2three('alanine')
+
+  puts "# Bio::AminoAcid.to_re('BZACDEFGHIKLMNPQRSTVWYU')"
+  p Bio::AminoAcid.to_re('BZACDEFGHIKLMNPQRSTVWYU')
+
+end
+