ngoto-bio 1.2.9.9001

data/bin/br_bioflat.rb

@@ -0,0 +1,293 @@
+#!/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

@@ -0,0 +1,45 @@
+#!/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
+