bio 1.5.1 → 2.0.2

data/bin/bioruby

@@ -1,47 +0,0 @@
-#!/usr/bin/env ruby
-#
-# = BioRuby shell - command line interface for the BioRuby library
-#
-# Copyright::   Copyright (C) 2005, 2006, 2007
-#               Toshiaki Katayama <k@bioruby.org>
-# License::     The Ruby License
-#
-# $Id:$
-#
-
-begin
-  require 'rubygems'
-  gem 'bio', '>= 1.1.0'
-rescue LoadError
-  require 'bio'
-end
-require 'bio/shell'
-
-# required to run commands (getseq, ls etc.)
-include Bio::Shell
-
-# setup command line options, working directory, and irb configurations
-Bio::Shell::Setup.new
-
-# loading workspace and command history
-Bio::Shell.load_session
-
-# sets default email address for Entrez eUtils.
-Bio::NCBI.default_email ||= 'staff@bioruby.org'
-
-# main loop
-if Bio::Shell.cache[:rails]
-  Bio::Shell.cache[:rails].join
-else
-  Signal.trap("SIGINT") do
-    Bio::Shell.cache[:irb].signal_handle
-  end
-
-  catch(:IRB_EXIT) do
-    Bio::Shell.cache[:irb].eval_input
-  end
-end
-
-# saving workspace, command history and configuration before exit
-Bio::Shell.save_session
-

data/bin/br_biofetch.rb

@@ -1,71 +0,0 @@
-#!/usr/bin/env ruby
-#
-# = biofetch - BioFetch client
-#
-# Copyright::   Copyright (C) 2002
-#               Toshiaki Katayama <k@bioruby.org>
-# License::     The Ruby License
-#
-#
-
-begin
-  require 'rubygems'
-rescue LoadError
-end
-
-require 'bio/io/fetch'
-
-def require_bio_old_biofetch_emulator(mandatory = true)
-  begin
-    require 'bio-old-biofetch-emulator'
-  rescue LoadError
-    if mandatory then
-      $stderr.puts "Error: please install bio-old-biofetch-emulator gem."
-      exit 1
-    end
-  end
-end
-
-def default_url
-  'http://bioruby.org/cgi-bin/biofetch.rb'
-end
-
-def another_url
-  'http://www.ebi.ac.uk/cgi-bin/dbfetch'
-end
-
-def usage
-  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
-  require_bio_old_biofetch_emulator(false)
-  ARGV.shift
-  serv = Bio::Fetch.new(ARGV.shift)
-  puts serv.fetch(*ARGV)
-when /^--?e/				# EBI server
-  ARGV.shift
-  serv = Bio::Fetch.new(another_url)
-  puts serv.fetch(*ARGV)
-when /^--?r/				# BioRuby server
-  require_bio_old_biofetch_emulator
-  ARGV.shift
-  serv = Bio::Fetch.new(default_url)
-  puts serv.fetch(*ARGV)
-else					# Default server
-  require_bio_old_biofetch_emulator
-  puts Bio::Fetch.query(*ARGV)
-end
-
-

data/bin/br_bioflat.rb

@@ -1,293 +0,0 @@
-#!/usr/bin/env ruby
-# 
-# = bioflat - OBDA flat file indexer (executable)
-# 
-# Copyright::   Copyright (C) 2002
-#               Naohisa Goto <ng@bioruby.org>
-# License::     The Ruby License
-#
-# $Id: br_bioflat.rb,v 1.17 2007/04/05 23:35:39 trevor 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
-                         (default: /usr/bin/sort or BUILTIN)
-  --env=/path/to/env     use env program to run sort (default: /usr/bin/env)
-  --env-arg=XXXXXX       argument given to the env program (default: LC_ALL=C)
-                         (multiple --env-arg=XXXXXX can be specified)
-
-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 /^\-\-?env\=(.*)/i
-      options['env_program'] = $1
-
-    when /^\-\-?env-arg(?:ument)?\=(.*)/i
-      options['env_program_arguments'] ||= []
-      options['env_program_arguments'].push $1
-
-    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
-

data/bin/br_biogetseq.rb

@@ -1,45 +0,0 @@
-#!/usr/bin/env ruby
-# 
-# = biogetseq - OBDA sequence data retrieval (executable)
-# 
-# Copyright::   Copyright (C) 2003
-#               Toshiaki Katayama <k@bioruby.org>
-# License::     The Ruby License
-#
-# $Id: br_biogetseq.rb,v 1.4 2007/04/05 23:35:39 trevor Exp $
-# 
-
-require 'bio'
-
-def usage
-  print <<END
-  #{$0} --dbname <dbname> [--namespace <namespace>] entry_id [entry_id]
-END
-  exit 1
-end
-
-if ARGV.size < 3
-  usage
-end
-
-while ARGV.first =~ /^-/
-  case ARGV.shift
-  when /^\-\-format/
-    ARGV.shift
-    raise NotImplementedError
-  when /^\-\-dbname/
-    dbname = ARGV.shift
-  when /^\-\-namespace/
-    namespace = ARGV.shift
-  end
-end
-
-reg = Bio::Registry.new
-db = reg.get_database(dbname)
-if namespace
-  db['namespace'] = namespace
-end
-ARGV.each do |entry|
-  puts db.get_by_id(entry)
-end
-