Class: Bio::DBGET

aaseq("db entry") method retrieves the amino acid sequence of the entry if any.

# File lib/bio/io/dbget.rb, line 142
  def DBGET.aaseq(arg)
    dbget("bget", "-f -n a #{arg}")
  end

alink(arg)

alink("db entry") method returns relations

[Source]

# File lib/bio/io/dbget.rb, line 100
  def DBGET.alink(arg)
    dbget("alink", arg)
  end

bfind(arg)

bfind("db keyword") method searches entries by keyword

[Source]

# File lib/bio/io/dbget.rb, line 105
  def DBGET.bfind(arg)
    dbget("bfind", arg)
  end

bget(arg)

bget("db entry") method retrieves entries specified by the entry names

[Source]

# File lib/bio/io/dbget.rb, line 110
  def DBGET.bget(arg)
    dbget("bget", arg)
  end

binfo(arg)

binfo("db") method retrieves the database information

[Source]

# File lib/bio/io/dbget.rb, line 147
  def DBGET.binfo(arg)
    dbget("binfo", arg)
  end

blink(arg)

blink("db entry") method retrieves the link information

[Source]

# File lib/bio/io/dbget.rb, line 152
  def DBGET.blink(arg)
    dbget("blink", arg)
  end

bman(arg)

bman ("db entry") method shows the manual page

[Source]

# File lib/bio/io/dbget.rb, line 157
  def DBGET.bman(arg)
    dbget("bman", arg)
  end

bref(arg)

bref("db entry") method retrieves the references and authors

[Source]

# File lib/bio/io/dbget.rb, line 162
  def DBGET.bref(arg)
    dbget("bref", arg)
  end

btab(arg)

btab ("db entry") method retrives (and generates) the database alias table

[Source]

# File lib/bio/io/dbget.rb, line 167
  def DBGET.btab(arg)
    dbget("btab", arg)
  end

btit(arg)

btit("db entry ..") method retrieves the entry definition

[Source]

# File lib/bio/io/dbget.rb, line 172
  def DBGET.btit(arg)
    dbget("btit", arg)
  end

dbget(com, arg, serv = nil, port = nil)

Main class method to access DBGET server. Optionally, this method can be called with the alternative DBGET server address and the TCP/IP port number.

‘com’ should be one of the following DBGET commands:

alink, bfind, bget, binfo, blink, bman, bref, btab, btit

These methods are shortcut for the dbget commands. Actually, Bio::DBGET.((|com|))(arg) internally calls Bio::DBGET.dbget(com, arg). Most of these methods accept the argument "-h" for help.

‘arg’ should be one of the following formats :

[options] db
- specify the database name only for binfo, bman etc.
[options] db:entry
- specify the database name and the entry name to retrieve.
[options] db entry1 entry2 …
- specify the database name and the list of entries to retrieve.

Note that options in the above example can be omitted. If ‘arg’ is empty, the help message with a list of options for ‘com’ will be shown by default. Supported database names will be found at the GenomeNet DBGET web page www.genome.jp/dbget/.

[Source]

# File lib/bio/io/dbget.rb, line 55
  def DBGET.dbget(com, arg, serv = nil, port = nil)

    unless serv or port         # if both of serv and port are nil
      if ENV["DBGET"] =~ /:/            # and ENV["DBGET"] exists
        serv, port = ENV["DBGET"].split(':')
      end
    end
    serv = serv ? serv : SERV
    port = port ? port : PORT

    if arg.empty?
      arg = "-h"                        # DBGET help message
    end

    query = "#{com} #{arg}\n"           # DBGET query string

    sock = TCPSocket.open("#{serv}", "#{port}")

    sock.write(query)                   # submit query
    sock.flush                  # buffer flush

    sock.gets                           # skip "+Helo DBgetServ ..."
    sock.gets                           # skip "#If you see this message, ..."
    sock.gets                           # skip "*Request-IDent"

    result = sock.read          # DBGET result

    sock.close

    return result
  end

naseq(arg)

naseq("db entry") method retrieves the nucleic acid sequence of the entry if any.

[Source]

# File lib/bio/io/dbget.rb, line 136
  def DBGET.naseq(arg)
    dbget("bget", "-f -n n #{arg}")
  end

seq(arg)

seq("db entry") method retrieves the first sequence of the entry

Shortcut to retrieve the sequence of the entry in FASTA format. This method is equivalent to Bio::DBGET.bget("-f -n 1 #{arg}") and ‘arg’ should be the "db:entry" or "db entry1 entry2 …" format.

[Source]

# File lib/bio/io/dbget.rb, line 119
  def DBGET.seq(arg)
    dbget("bget", "-f -n 1 #{arg}")
  end

seq2(arg)

seq2("db entry") method retrieves the second sequence of the entry if any

Shortcut to retrieve the second sequence of the entry in FASTA format. This method is equivalent to Bio::DBGET.bget("-f -n 2 #{arg}"). Only useful when treating the KEGG GENES database entries which have both AASEQ and NTSEQ fields. This method is obsolete and it is recommended to use ‘naseq’ and ‘aaseq’ instead.

[Source]

# File lib/bio/io/dbget.rb, line 130
  def DBGET.seq2(arg)
    dbget("bget", "-f -n 2 #{arg}")
  end

version()

Show the version information of the DBGET server.

[Source]

# File lib/bio/io/dbget.rb, line 88
  def DBGET.version
    dbget("bget", "-V")
  end

SERV	=	"dbget.genome.jp"		default DBGET server address SERV = "dbgetserv.genome.jp"
PORT	=	"3266"		default DBGET port number

Methods

Constants

Public Class methods