* lib/bio/io/flatfile/indexer.rb is included in bio.rb

bioruby · Sep 15, 2017 · 1b022f6 · 1b022f6
1 parent 00cf41f
commit 1b022f6
Showing 1 changed file with 61 additions and 67 deletions.
diff --git a/bin/br_bioflat.rb b/bin/br_bioflat.rb
@@ -18,87 +18,81 @@
 #  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 1.2 2002/08/21 18:01:26 ng Exp $ 
+#  $Id: br_bioflat.rb,v 1.3 2002/08/26 06:08:20 k Exp $ 
 # 
 
 require 'bio'
-require 'bio/io/flatfile/indexer'
 
-#if __FILE__ == $0
-if true
-
-  def create_index(is_bdb, dbname, format, *files)
-    case format
-    when /genbank/i
-      dbclass = Bio::GenBank
-      add_secondary = nil
-    when /genpept/i
-      dbclass = Bio::GenPept
-      add_secondary = nil
-    when /embl/i
-      dbclass = Bio::EMBL
-      add_secondary = [ 'DR' ]
-    when /sptr/i
-      dbclass = Bio::SPTR
-      add_secondary = [ 'DR' ]
-    else
-      raise "Unsupported format : #{format}"
-    end
-    if is_bdb then
-      Bio::FlatFileIndex::Indexer::makeindexBDB(dbname, dbclass, nil, nil, add_secondary, *files)
-    else
-      Bio::FlatFileIndex::Indexer::makeindexFlat(dbname, dbclass, nil, nil, add_secondary, *files)
-    end
+def create_index(is_bdb, dbname, format, *files)
+  case format
+  when /genbank/i
+    dbclass = Bio::GenBank
+    add_secondary = nil
+  when /genpept/i
+    dbclass = Bio::GenPept
+    add_secondary = nil
+  when /embl/i
+    dbclass = Bio::EMBL
+    add_secondary = [ 'DR' ]
+  when /sptr/i
+    dbclass = Bio::SPTR
+    add_secondary = [ 'DR' ]
+  else
+    raise "Unsupported format : #{format}"
   end
-
-  def do_index
-    is_bdb = (/bdb/i).match(ARGV[0]) ? Bio::FlatFileIndex::MAGIC_BDB : nil
-    dbname = ARGV[1]
-    format = ARGV[3]
-    files  = ARGV[4..-1]
-    files.shift if files[0] == '--files'
-    create_index(is_bdb, dbname, format, *files)
+  if is_bdb then
+    Bio::FlatFileIndex::Indexer::makeindexBDB(dbname, dbclass, nil, nil, add_secondary, *files)
+  else
+    Bio::FlatFileIndex::Indexer::makeindexFlat(dbname, dbclass, nil, nil, add_secondary, *files)
   end
+end
 
 
-  def do_search
-    ARGV.shift if ARGV[0] == '--search'
-    dbname = ARGV.shift
-    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
-    end
-    db.close
-  end
+def do_index
+  is_bdb = (/bdb/i).match(ARGV[0]) ? Bio::FlatFileIndex::MAGIC_BDB : nil
+  dbname = ARGV[1]
+  format = ARGV[3]
+  files  = ARGV[4..-1]
+  files.shift if files[0] == '--files'
+  create_index(is_bdb, dbname, format, *files)
+end
 
 
-  def usage
-    print "Create index: \n"
-    print "#{$0} --makeindex DBNAME --format CLASS [--files] FILENAME...\n"
-    print "#{$0} --makeindexBDB DBNAME --format CLASS [--files] FILENAME...\n"
-    print "Search: \n"
-    print "#{$0} [--search] DBNAME KEYWORD...\n"
+def do_search
+  ARGV.shift if ARGV[0] == '--search'
+  dbname = ARGV.shift
+  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
   end
+  db.close
+end
 
 
-  if ARGV.size > 1
-    case ARGV[0]
-    when /--make/
-      do_index
-    when /--search/
-      do_search
-    else #default is search
-      do_search
-    end
-  else
-    usage
-  end
+def usage
+  print "Create index: \n"
+  print "#{$0} --makeindex DBNAME --format CLASS [--files] FILENAME...\n"
+  print "#{$0} --makeindexBDB DBNAME --format CLASS [--files] FILENAME...\n"
+  print "Search: \n"
+  print "#{$0} [--search] DBNAME KEYWORD...\n"
+end
 
 
+if ARGV.size > 1
+  case ARGV[0]
+  when /--make/
+    do_index
+  when /--search/
+    do_search
+  else #default is search
+    do_search
+  end
+else
+  usage
 end