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Bio::DBGET

Constants

PORT

default DBGET port number

SERV

default DBGET server address SERV = “dbgetserv.genome.jp”

Public Class Methods

aaseq(arg) click to toggle source

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
bfind(arg) click to toggle source

bfind(“db keyword”) method searches entries by keyword

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

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

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

binfo(“db”) method retrieves the database information

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

bman (“db entry”) method shows the manual page

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

bref(“db entry”) method retrieves the references and authors

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

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

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

btit(“db entry ..”) method retrieves the entry definition

# File lib/bio/io/dbget.rb, line 172
def DBGET.btit(arg)
  dbget("btit", arg)
end
dbget(com, arg, serv = nil, port = nil) click to toggle source

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/.

# 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) click to toggle source

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

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

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.

# File lib/bio/io/dbget.rb, line 119
def DBGET.seq(arg)
  dbget("bget", "-f -n 1 #{arg}")
end
seq2(arg) click to toggle source

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.

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

Show the version information of the DBGET server.

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

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