bio 0.7.0

data/bin/bioruby

@@ -0,0 +1,107 @@
+#!/usr/bin/env ruby
+#
+# = BioRuby shell - command line interface for the BioRuby library
+#
+# Copyright::	Copyright (C) 2005
+#		Toshiaki Katayama <k@bioruby.org>
+# License::	LGPL
+#
+# $Id: bioruby,v 1.10 2005/12/07 05:12:06 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
+#
+#++
+#
+
+# $: << File.dirname(__FILE__)+'/../lib'
+
+begin
+  require 'rubygems'
+  require_gem 'bio', '~> 0.7'
+rescue LoadError
+end
+
+require 'bio/shell'
+
+include Bio::Shell
+
+# loading configuration and plugins
+Bio::Shell.setup
+
+### IRB setup
+
+require 'irb'
+begin
+  require 'irb/completion'
+  Bio::Shell.cache[:readline] = true
+rescue LoadError
+  Bio::Shell.cache[:readline] = false
+end
+
+IRB.setup(nil)
+
+# set application name
+IRB.conf[:AP_NAME] = 'bioruby'
+
+# change prompt for bioruby
+$_ = Bio::Shell.esc_seq
+IRB.conf[:PROMPT][:BIORUBY_COLOR] = {
+  :PROMPT_I => "bio#{$_[:ruby]}ruby#{$_[:none]}> ",
+  :PROMPT_S => "bio#{$_[:ruby]}ruby#{$_[:none]}%l ",
+  :PROMPT_C => "bio#{$_[:ruby]}ruby#{$_[:none]}+ ",
+  :RETURN   => "  ==> %s\n"
+}
+IRB.conf[:PROMPT][:BIORUBY] = {
+  :PROMPT_I => "bioruby> ",
+  :PROMPT_S => "bioruby%l ",
+  :PROMPT_C => "bioruby+ ",
+  :RETURN   => "  ==> %s\n"
+}
+if Bio::Shell.config[:color]
+  IRB.conf[:PROMPT_MODE] = :BIORUBY_COLOR
+else
+  IRB.conf[:PROMPT_MODE] = :BIORUBY
+end
+IRB.conf[:ECHO] = Bio::Shell.config[:echo] || false
+
+# irb/input-method.rb >= v1.5 (not in 1.8.2)
+#IRB.conf[:SAVE_HISTORY] = 100000
+
+# not beautifully works
+#IRB.conf[:AUTO_INDENT] = true
+
+### IRB main loop
+
+irb = IRB::Irb.new
+
+# needed for method completion
+IRB.conf[:MAIN_CONTEXT] = irb.context
+
+# loading workspace and command history
+Bio::Shell.load
+
+Signal.trap("SIGINT") do
+  irb.signal_handle
+end
+
+catch(:IRB_EXIT) do
+  irb.eval_input
+end
+
+# saving workspace, command history and configuration before exit
+Bio::Shell.save
+

data/bin/br_biofetch.rb

@@ -0,0 +1,59 @@
+#!/usr/bin/env ruby
+#
+# biofetch - BioFetch client
+#
+#   Copyright (C) 2002 KATAYAMA Toshiaki <k@bioruby.org>
+#
+#  This program is free software; you can redistribute it and/or modify
+#  it under the terms of the GNU General Public License as published by
+#  the Free Software Foundation; either version 2 of the License, or
+#  (at your option) any later version.
+#
+#  This program 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 General Public License for more details.
+#
+#  You should have received a copy of the GNU General Public License
+#  along with this program; if not, write to the Free Software
+#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+#
+#  $Id: br_biofetch.rb,v 1.2 2002/12/03 18:54:43 k Exp $
+#
+
+require 'bio/io/fetch'
+
+def usage
+  default_url = 'http://bioruby.org/cgi-bin/biofetch.rb'
+  another_url = 'http://www.ebi.ac.uk/cgi-bin/dbfetch'
+  puts "#{$0} [-s[erver] #{another_url}] db id [style] [format]"
+  puts "  server : URL of the BioFetch CGI (default is #{default_url})"
+  puts "      db : database name (embl, genbank, etc.)"
+  puts "      id : entry id"
+  puts "   style : 'raw' or 'html' (default is 'raw')"
+  puts "  format : change the output format ('default', 'fasta', etc.)"
+end
+
+if ARGV.empty? or ARGV[0] =~ /^--?h/
+  usage
+  exit 1
+end
+
+case ARGV[0]
+when /^--?s/				# User specified server
+  ARGV.shift
+  serv = Bio::Fetch.new(ARGV.shift)
+  puts serv.fetch(*ARGV)
+when /^--?e/				# EBI server
+  ARGV.shift
+  serv = Bio::Fetch.new('http://www.ebi.ac.uk/cgi-bin/dbfetch')
+  puts serv.fetch(*ARGV)
+when /^--?r/				# BioRuby server
+  ARGV.shift
+  serv = Bio::Fetch.new('http://bioruby.org/cgi-bin/biofetch.rb')
+  puts serv.fetch(*ARGV)
+else					# Default server
+  puts Bio::Fetch.query(*ARGV)
+end
+
+

data/bin/br_bioflat.rb

@@ -0,0 +1,294 @@
+#!/usr/bin/env ruby
+# 
+# bioflat - OBDA flat file indexer (executable)
+# 
+#   Copyright (C) 2002 GOTO Naohisa <ngoto@gen-info.osaka-u.ac.jp> 
+# 
+#  This program is free software; you can redistribute it and/or modify 
+#  it under the terms of the GNU General Public License as published by 
+#  the Free Software Foundation; either version 2 of the License, or 
+#  (at your option) any later version. 
+# 
+#  This program 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 General Public License for more details. 
+# 
+#  You should have received a copy of the GNU General Public License 
+#  along with this program; if not, write to the Free Software 
+#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA 
+# 
+#  $Id: br_bioflat.rb,v 1.14 2003/08/27 17:28:30 ng Exp $ 
+# 
+
+require 'bio'
+
+def usage
+  print <<EOM
+Search:
+  #{$0} [--search] [options...] [DIR/]DBNAME KEYWORDS
+or
+  #{$0} [--search] --location DIR --dbname DBNAME [options...] KEYWORDS
+
+Search options:
+  --namespace NAME       set serch namespace to NAME
+  (or --name NAME)         You can set this option many times to specify
+                           more than one namespace.
+
+Create index:
+  #{$0} --create --location DIR --dbname DBNAME [--format <genbank|embl|fasta>] [options...] [--files] FILES
+Update index:
+  #{$0} --update --location DIR --dbname DBNAME [options...] [--files] FILES
+
+Create index options:
+  --primary=UNIQUE       set primary namespece to UNIQUE
+                           Default primary/secondary namespaces depend on
+                           each format of flatfiles.
+  --secondary=KEY        set secondary namespaces.
+                           You may use this option many times to specify
+                           more than one namespace.
+  --add-secondary=KEY    add secondary namespaces to default specification.
+                           You can use this option many times.
+
+Options only valid for --create (or --update) --type flat:
+  --sort=/path/to/sort   use external sort program (e.g. /usr/bin/sort)
+  --sort=BUILTIN         use builtin sort routine
+
+Options only valid for --update:
+  --renew                re-read all flatfiles and update whole index
+
+Backward compatibility:
+  --makeindex DIR/DBNAME
+      same as --create --type flat --location DIR --dbname DBNAME
+  --makeindexBDB DIR/DBNAME
+      same as --create --type bdb  --location DIR --dbname DBNAME
+  --format=CLASS
+      instead of genbank|embl|fasta, specifing a class name is allowed
+
+Show namespaces:
+  #{$0} --show-namespaces [--location DIR --dbname DBNAME] [DIR/DBNAME]
+or
+  #{$0} --show-namespaces [--format=CLASS]
+or
+  #{$0} --show-namespaces --files file
+
+EOM
+
+end
+
+
+def do_index(mode = :create)
+  case ARGV[0]
+  when /^\-\-?make/
+    dbpath = ARGV[1]
+    args = ARGV[2..-1]
+    is_bdb = nil
+  when /^\-\-?make.*bdb/i
+    dbname = ARGV[1]
+    args = ARGV[2..-1]
+    is_bdb = Bio::FlatFileIndex::MAGIC_BDB
+  when /^\-\-create/, /^\-\-update/
+    args = ARGV[1..-1]
+  else
+    usage
+  end
+
+  options = {}
+
+  while args.first =~ /^\-/
+    case x = args.shift
+
+    # OBDA stuff
+
+    when /^\-\-?format/
+      args.shift
+      format = nil		# throw this f*ckin' mess for auto detect :)
+    when /^\-\-?location/
+      location = args.shift.chomp('/')
+    when /^\-\-?dbname/
+      dbname = args.shift
+    when /^\-\-?(index)?type/
+      indextype = args.shift
+      case indextype
+      when /bdb/
+	is_bdb = Bio::FlatFileIndex::MAGIC_BDB
+      when /flat/
+	is_bdb = nil
+      else
+	usage
+      end
+
+    # BioRuby extension
+
+    when /^\-\-?files/i
+      break
+
+    when /^\-\-?format\=(.*)/i
+      format = $1
+
+    when /^\-\-?sort\=(.*)/i
+      options['sort_program'] = $1
+      options['onmemory'] = nil
+    when /^\-\-?no\-?te?mp/i
+      options['onmemory'] = true
+
+    when /^\-\-?primary.*\=(.*)/i
+      options['primary_namespace'] = $1
+
+    when /^\-\-?add-secondary.*\=(.*)/i
+      unless options['additional_secondary_namespaces'] then
+	options['additional_secondary_namespaces'] = []
+      end
+      options['additional_secondary_namespaces'] << $1 if $1.length > 0
+
+    when /^\-\-?secondary.*\=(.*)/i
+      unless options['secondary_namespaces'] then
+	options['secondary_namespaces'] = []
+      end
+      options['secondary_namespaces'] << $1 if $1.length > 0
+
+    when /^\-\-?renew/
+      options['renew'] = true
+
+    else
+      STDERR.print "Warning: ignoring invalid option #{x.inspect}\n"
+    end
+  end
+
+  dbpath = File.join(location, dbname) unless dbpath
+  if mode == :update then
+    Bio::FlatFileIndex::update_index(dbpath, format, options, *args)
+  else
+    Bio::FlatFileIndex::makeindex(is_bdb, dbpath, format, options, *args)
+  end
+end
+
+
+def do_search
+  dbname = nil
+  location = nil
+  names = []
+  while x = ARGV.shift
+    case x
+    when /\A\-\-?search/i
+      #do nothing
+    when /\A\-\-?location/i
+      location = ARGV.shift.to_s.chomp('/')
+    when /\A\-\-?dbname/i
+      dbname = ARGV.shift
+    when /\A\-\-?name(?:space)?(?:\=(.+))?/i
+      if $1 then
+	names << $1
+      elsif x = ARGV.shift
+	names << x
+      end
+    else
+      ARGV.unshift x
+      break
+    end
+  end
+  dbname = ARGV.shift unless dbname
+  dbname = File.join(location, dbname) unless location.to_s.empty?
+  db = Bio::FlatFileIndex.open(dbname)
+  ARGV.each do |key|
+    STDERR.print "Searching for \'#{key}\'...\n"
+    #r = db.search(key)
+    #STDERR.print "OK, #{r.size} entry found\n"
+    #if r.size > 0 then
+    #  print r
+    #end
+    begin
+      if names.empty? then
+	r = db.include?(key)
+      else
+	r = db.include_in_namespaces?(key, *names)
+      end
+    rescue RuntimeError
+      STDERR.print "ERROR: #{$!}\n"
+      next
+    end
+    r = [] unless r
+    STDERR.print "OK, #{r.size} entry found\n"
+    r.each do |i|
+      print db.search_primary(i)
+    end
+  end
+  db.close
+end
+
+
+def do_show_namespaces
+  dbname = nil
+  location = nil
+  files = nil
+  format = nil
+  names = []
+  while x = ARGV.shift
+    case x
+    when /\A\-\-?(show\-)?name(space)?s/i
+      #do nothing
+    when /\A\-\-?location/i
+      location = ARGV.shift.to_s.chomp('/')
+    when /\A\-\-?dbname/i
+      dbname = ARGV.shift
+    when /\A\-\-?format(?:\=(.+))?/i
+      if $1 then
+	format = $1
+      elsif x = ARGV.shift
+	format = x
+      end
+    when /\A\-\-?files/i
+      files = ARGV
+      break
+    else
+      ARGV.unshift x
+      break
+    end
+  end
+  if files then
+    k = nil
+    files.each do |x|
+      k = Bio::FlatFile.autodetect_file(x)
+      break if k
+    end
+    if k then
+      STDERR.print "Format: #{k.to_s}\n"
+      format = k
+    else
+      STDERR.print "ERROR: couldn't determine file format\n"
+      return
+    end
+  end
+  STDERR.print "Namespaces: (first line: primary namespace)\n"
+  if format then
+    parser = Bio::FlatFileIndex::Indexer::Parser.new(format)
+    print parser.primary.name, "\n"
+    puts parser.secondary.keys
+  else
+    dbname = ARGV.shift unless dbname
+    dbname = File.join(location, dbname) unless location.to_s.empty?
+    db = Bio::FlatFileIndex.open(dbname)
+    puts db.namespaces
+    db.close
+  end
+end
+
+if ARGV.size > 1
+  case ARGV[0]
+  when /--make/, /--create/
+    Bio::FlatFileIndex::DEBUG.out = true
+    do_index
+  when /--update/
+    Bio::FlatFileIndex::DEBUG.out = true
+    do_index(:update)
+  when /\A\-\-?(show\-)?name(space)?s/i
+    do_show_namespaces
+  when /--search/
+    do_search
+  else #default is search
+    do_search
+  end
+else
+  usage
+end
+