bio 1.0.0 → 1.1.0

data/lib/bio/appl/sim4.rb

@@ -2,25 +2,9 @@
 # = bio/appl/sim4.rb - sim4 wrapper class
 #
 # Copyright:: Copyright (C) 2004 GOTO Naohisa <ng@bioruby.org>
-# License::   LGPL
+# License::   The Ruby License
 #
-#--
-#  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
-#++
-#
-#  $Id: sim4.rb,v 1.5 2005/12/18 15:58:40 k Exp $
+#  $Id: sim4.rb,v 1.10 2007/04/05 23:35:39 trevor Exp $
 #
 # The sim4 execution wrapper class.
 #
@@ -31,8 +15,8 @@
 #   http://www.genome.org/cgi/content/abstract/8/9/967
 #
 
-require 'open3'
 require 'tempfile'
+require 'bio/command'
 
 module Bio
 
@@ -45,14 +29,13 @@ module Bio
     # [+program+]  Program name. Usually 'sim4' in UNIX.
     # [+database+] Default file name of database('seq2').
     # [+option+]   Options (array of strings).
-    def initialize(program = 'sim4', database = nil, option = [])
+    def initialize(program = 'sim4', database = nil, opt = [])
       @program = program
-      @option = option
+      @options = opt
       @database = database #seq2
       @command = nil
       @output = nil
       @report = nil
-      @log = nil
     end
 
     # default file name of database('seq2')
@@ -62,13 +45,27 @@ module Bio
     attr_reader :program
 
     # options
-    attr_reader :option
+    attr_accessor :options
+
+    # option is deprecated. Instead, please use options.
+    def option
+      warn "option is deprecated. Please use options."
+      options
+    end
 
     # last command-line strings executed by the object
     attr_reader :command
 
+    #---
     # last messages of program reported to the STDERR
-    attr_reader :log
+    #attr_reader :log
+    #+++
+
+    #log is deprecated (no replacement) and returns empty string.
+    def log
+      warn "log is deprecated (no replacement) and returns empty string."
+      ''
+    end
 
     # last result text (String)
     attr_reader :output
@@ -110,20 +107,13 @@ module Bio
     # <tt>filename1</tt> and <tt>filename2</tt> should be file name strings.
     # If <tt>filename2</tt> is not specified, using <tt>self.database</tt>.
     def exec_local(filename1, filename2 = nil)
-      @command = [ @program, filename1, (filename2 or @database), *@option ]
+      @command = [ @program, filename1, (filename2 or @database), *@options ]
       @output = nil
-      @log = nil
       @report = nil
-      Open3.popen3(*@command) do |din, dout, derr|
-        din.close
-        derr.sync = true
-        t = Thread.start { @log = derr.read }
-        begin
-          @output = dout.read
-          @report = Bio::Sim4::Report.new(@output)
-        ensure
-          t.join
-        end
+      Bio::Command.call_command(@command) do |io|
+        io.close_write
+        @output = io.read
+        @report = Bio::Sim4::Report.new(@output)
       end
       @report
     end

data/lib/bio/appl/sim4/report.rb

@@ -2,25 +2,9 @@
 # = bio/appl/sim4/report.rb - sim4 result parser
 #
 # Copyright:: Copyright (C) 2004 GOTO Naohisa <ng@bioruby.org>
-# License::   LGPL
+# License::   The Ruby License
 #
-#--
-#  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
-#++
-#
-#  $Id: report.rb,v 1.7 2005/12/18 15:58:40 k Exp $
+#  $Id: report.rb,v 1.9 2007/04/05 23:35:40 trevor Exp $
 #
 # The sim4 report parser classes.
 #

data/lib/bio/appl/sosui/report.rb

@@ -1,32 +1,17 @@
 #
 # = bio/appl/sosui/report.rb - SOSUI report class
 # 
-# Copyright::   Copyright (C) 2003 Mitsuteru C. Nakao <n@bioruby.org>
-# License::     LGPL
+# Copyright::   Copyright (C) 2003 
+#               Mitsuteru C. Nakao <n@bioruby.org>
+# License::     The Ruby License
 #
-#  $Id: report.rb,v 1.9 2005/12/18 15:58:41 k Exp $
+#  $Id: report.rb,v 1.11 2007/04/05 23:35:40 trevor Exp $
 #
 # == Example
 #
 # == References
-# * http://sosui.proteome.bio.tuat.ac.jp/sosui_submit.html
-#--
-#
-#  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
-#
-#++
+# * http://sosui.proteome.bio.tuat.ac.jp/sosui_submit.html
 #
 
 

data/lib/bio/appl/spidey/report.rb

@@ -2,9 +2,9 @@
 # = bio/appl/spidey/report.rb - SPIDEY result parser
 #
 # Copyright:: Copyright (C) 2004 GOTO Naohisa <ng@bioruby.org>
-# License::   Ruby's
+# License::   The Ruby License
 #
-#  $Id: report.rb,v 1.9 2006/02/22 08:46:15 ngoto Exp $
+#  $Id: report.rb,v 1.10 2007/04/05 23:35:40 trevor Exp $
 #
 # NCBI Spidey result parser.
 # Currently, output of default (-p 0 option) or -p 1 option are supported.

data/lib/bio/appl/targetp/report.rb

@@ -1,10 +1,11 @@
 #
 # = bio/appl/targetp/report.rb - TargetP report class
 # 
-# Copyright::  Copyright (C) 2003 Mitsuteru C. Nakao <n@bioruby.org>
-# License::    LGPL
+# Copyright::  Copyright (C) 2003 
+#              Mitsuteru C. Nakao <n@bioruby.org>
+# License::    The Ruby License
 #
-#  $Id: report.rb,v 1.7 2005/12/18 15:58:41 k Exp $
+#  $Id: report.rb,v 1.9 2007/04/05 23:35:40 trevor Exp $
 #
 # == Description
 #
@@ -12,23 +13,6 @@
 #
 # == Example
 # == References
-#--
-#
-#  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

data/lib/bio/appl/tcoffee.rb

@@ -0,0 +1,55 @@
+#
+# = bio/appl/tcoffee.rb - T-Coffee application wrapper class
+#
+# Copyright:: Copyright (C) 2006-2007
+#             Jeffrey Blakeslee and John Conery University of Oregon <jeffb@uoregon.edu>
+#             Naohisa Goto <ng@bioruby.org>
+# License::   The Ruby License
+#
+#  $Id: tcoffee.rb,v 1.1 2007/07/16 12:25:50 ngoto Exp $
+#
+# Bio::Tcoffee is a wrapper class to execute T-Coffee.
+#
+# == References
+#
+# * http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html
+# * Notredame, C., Higgins, D.G. and Heringa, J.
+#   T-Coffee: A novel method for fast and accurate multiple sequence
+#   alignment. J. Mol. Biol. 302: 205-217, 2000.
+#
+
+
+module Bio
+
+  # Bio::Tcoffee is a wrapper class to execute t-coffee.
+  #
+  # Please refer documents in bio/apple/tcoffee.rb for references.
+  class Tcoffee < Bio::Alignment::FactoryTemplate::FileInFileOutWithTree
+
+    # default program name
+    DEFAULT_PROGRAM = 't_coffee'.freeze
+
+    # default report parser
+    DEFAULT_PARSER = Bio::ClustalW::Report
+
+    private
+    # generates options specifying input filename.
+    # returns an array of string
+    def _option_input_file(fn)
+      [ '-infile', fn ]
+    end
+
+    # generates options specifying output filename.
+    # returns an array of string
+    def _option_output_file(fn)
+      [ '-outfile', fn ]
+    end
+
+    # generates options specifying output filename.
+    # returns an array of string
+    def _option_output_dndfile(fn)
+      [ '-newtree', fn ]
+    end
+  end #class TCoffee
+
+end #module Bio

data/lib/bio/appl/tmhmm/report.rb

@@ -1,33 +1,17 @@
 #
 # = bio/appl/tmhmm/report.rb - TMHMM report class
 # 
-# Copyright::  Copyright (C) 2003 Mitsuteru C. Nakao <n@bioruby.org>
-# License::    LGPL
+# Copyright::  Copyright (C) 2003 
+#              Mitsuteru C. Nakao <n@bioruby.org>
+# License::    The Ruby License
 #
-#  $Id: report.rb,v 1.6 2005/12/18 15:58:41 k Exp $
+#  $Id: report.rb,v 1.8 2007/04/05 23:35:40 trevor Exp $
 #
 # == Description
 #
 #
 # == Example
 # == References
-#--
-#
-#  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

data/lib/bio/command.rb

@@ -1,51 +1,35 @@
 #
 # = bio/command.rb - general methods for external command execution
 #
-# Copyright::	Copyright (C) 2003-2005
+# Copyright::	Copyright (C) 2003-2006
 # 		Naohisa Goto <ng@bioruby.org>,
 #		Toshiaki Katayama <k@bioruby.org>
-# License::	LGPL
+# License::	The Ruby License
 #
-#  $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
-#
-#++
+#  $Id: command.rb,v 1.17 2007/04/05 23:35:39 trevor Exp $
 #
 
 require 'open3'
+require 'uri'
+require 'open-uri'
+require 'net/http'
 
 module Bio
-module Command
 
-# = Bio::Command::Tools
+# = Bio::Command
+#
+# Bio::Command is a collection of useful methods for execution
+# of external commands or web applications.
+# Any wrapper class for applications shall use this class.
 #
-# 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
+# Library internal use only. Users should not directly use it.
+module Command
 
   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
+  module_function
 
   # Escape special characters in command line string for cmd.exe on Windows.
   def escape_shell_windows(str)
@@ -98,69 +82,256 @@ module Tools
   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)
+  # environment and fork for the others.
+  # A block must be given. An IO object is passed to the block.
+  def call_command(cmd, &block)
     case RUBY_PLATFORM
     when /mswin32|bccwin32/
-      call_command_local_popen(cmd, query, &block)
+      call_command_popen(cmd, &block)
     else
-      call_command_local_open3(cmd, query, &block)
+      call_command_fork(cmd, &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)
+  # A block must be given. An IO object is passed to the block.
+  def call_command_popen(cmd)
     str = make_command_line(cmd)
     IO.popen(str, "w+") do |io|
-      if block_given? then
-        io.sync = true
-        yield io, io
+      io.sync = true
+      yield io
+    end
+  end
+
+  # Executes the program via fork (by using IO.popen("-")) and exec.
+  # A block must be given. An IO object is passed to the block.
+  #
+  # From the view point of security, this method is recommended
+  # rather than call_command_popen.
+  def call_command_fork(cmd)
+    IO.popen("-", "r+") do |io|
+      if io then
+        # parent
+        yield io
       else
+        # child
+        begin
+          Kernel.exec(*cmd)
+        rescue Errno::ENOENT, Errno::EACCES
+          Process.exit!(127)
+        rescue Exception
+        end
+        Process.exit!(1)
+      end
+    end
+  end
+
+  # Executes the program via Open3.popen3
+  # A block must be given. IO objects are passed to the block.
+  #
+  # You would use this method only when you really need to get stderr.
+  def call_command_open3(cmd)
+    cmd = cmd.collect { |x| x.to_s }
+    Open3.popen3(*cmd) do |pin, pout, perr|
+      yield pin, pout, perr
+    end
+  end
+
+  # Executes the program with the query (String) given to the standard input,
+  # waits the program termination, and returns the output data printed to the
+  # standard output as a string.
+  # 
+  # Automatically select popen for Windows environment and fork for the others.
+  def query_command(cmd, query = nil)
+    case RUBY_PLATFORM
+    when /mswin32|bccwin32/
+      query_command_popen(cmd, query)
+    else
+      query_command_fork(cmd, query)
+    end
+  end
+
+  # Executes the program with the query (String) given to the standard input,
+  # waits the program termination, and returns the output data printed to the
+  # standard output as a string.
+  #
+  # IO.popen is used for OS which doesn't support fork.
+  def query_command_popen(cmd, query = nil)
+    str = make_command_line(cmd)
+    IO.popen(str, "w+") do |io|
+      io.sync = true
+      io.print query if query
+      io.close_write
+      io.read
+    end
+  end
+
+  # Executes the program with the query (String) given to the standard input,
+  # waits the program termination, and returns the output data printed to the
+  # standard output as a string.
+  #
+  # Fork (by using IO.popen("-")) and exec is used to execute the program.
+  #
+  # From the view point of security, this method is recommended
+  # rather than query_popen.
+  def query_command_fork(cmd, query = nil)
+    IO.popen("-", "r+") do |io|
+      if io then
+        # parent
         io.sync = true
         io.print query if query
         io.close_write
         io.read
+      else
+        # child
+        begin
+          Kernel.exec(*cmd)
+        rescue Errno::ENOENT, Errno::EACCES
+          Process.exit!(127)
+        rescue Exception
+        end
+        Process.exit!(1)
       end
     end
   end
 
-  # Executes the program via Open3.popen3
-  # If block is given, yield the block with input and output IO objects.
+  # Executes the program via Open3.popen3 with the query (String) given
+  # to the stain, waits the program termination, and
+  # returns the data from stdout and stderr as an array of the strings.
   #
   # From the view point of security, this method is recommended
   # rather than exec_local_popen.
-  def call_command_local_open3(cmd, query = nil)
+  def query_command_open3(cmd, query = nil)
+    errorlog = 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
+      t = Thread.start { errorlog = perr.read }
+      begin
+        pin.print query if query
+        pin.close
+        output = pout.read
+      ensure
+        t.join
       end
+      [ output, errorlog ]
+    end
+  end
+
+  # Same as OpenURI.open_uri(uri).read.
+  def read_uri(uri)
+    OpenURI.open_uri(uri).read
+  end
+
+  # Same as:
+  #   Net::HTTP.start(address, port)
+  # and 
+  # it uses proxy if an environment variable (same as OpenURI.open_uri)
+  # is set.
+  #
+  def start_http(address, port = 80, &block)
+    uri = URI.parse("http://#{address}:#{port}")
+    # Note: URI#find_proxy is an unofficial method defined in open-uri.rb.
+    # If the spec of open-uri.rb would be changed, we should change below.
+    if proxyuri = uri.find_proxy then
+      raise 'Non-HTTP proxy' if proxyuri.class != URI::HTTP
+      http = Net::HTTP.Proxy(proxyuri.host, proxyuri.port)
+    else
+      http = Net::HTTP
     end
+    http.start(address, port, &block)
   end
 
-  # Shows the latest stderr of the program execution.
-  # Note that this method may be thread unsafe.
-  attr_reader :errorlog
-  public :errorlog
+  # Same as:
+  #   Net::HTTP.new(address, port)
+  # and 
+  # it uses proxy if an environment variable (same as OpenURI.open_uri)
+  # is set.
+  #
+  def new_http(address, port = 80)
+    uri = URI.parse("http://#{address}:#{port}")
+    # Note: URI#find_proxy is an unofficial method defined in open-uri.rb.
+    # If the spec of open-uri.rb would be changed, we should change below.
+    if proxyuri = uri.find_proxy then
+      raise 'Non-HTTP proxy' if proxyuri.class != URI::HTTP
+      Net::HTTP.new(address, port, proxyuri.host, proxyuri.port)
+    else
+      Net::HTTP.new(address, port)
+    end
+  end
+
+  # Same as:
+  # Net::HTTP.post_form(uri, params)
+  # and 
+  # it uses proxy if an environment variable (same as OpenURI.open_uri)
+  # is set.
+  # In addition, +header+ can be set.
+  # (Note that Content-Type and Content-Length are automatically
+  # set by default.)
+  # +uri+ must be a URI object, +params+ must be a hash, and
+  # +header+ must be a hash.
+  #
+  def post_form(uri, params = nil, header = {})
+    unless uri.is_a?(URI)
+      uri = URI.parse(uri)
+    end
+
+    data = make_cgi_params(params)
+
+    hash = {
+      'Content-Type'   => 'application/x-www-form-urlencoded',
+      'Content-Length' => data.length.to_s
+    }
+    hash.update(header)
+
+    start_http(uri.host, uri.port) do |http|
+      http.post(uri.path, data, hash)
+    end
+  end
+
+  def make_cgi_params(params)
+    data = ""
+    case params
+    when Hash
+      data = params.map do |key, val|
+        make_cgi_params_key_value(key, val)
+      end.join('&')
+    when Array
+      case params.first
+      when Hash
+        data = params.map do |hash|
+          hash.map do |key, val|
+            make_cgi_params_key_value(key, val)
+          end
+        end.join('&')
+      when Array
+        data = params.map do |key, val|
+          make_cgi_params_key_value(key, val)
+        end.join('&')
+      when String
+        data = params.map do |str|
+          URI.escape(str.strip)
+        end.join('&')
+      end
+    when String
+      data = URI.escape(params.strip)
+    end
+    return data
+  end
+
+  def make_cgi_params_key_value(key, value)
+    result = []
+    case value
+    when Array
+      value.each do |val|
+        result << [key, val].map {|x| URI.escape(x.to_s) }.join('=')
+      end
+    else
+      result << [key, value].map {|x| URI.escape(x.to_s) }.join('=')
+    end
+    return result
+  end
 
-end # module Tools
 end # module Command
 end # module Bio