Class: Bio::DBGET

Inherits:
Object show all
Defined in:
lib/bio/io/dbget.rb

Constant Summary

SERV =

default DBGET server address

"dbget.genome.jp"
PORT =

default DBGET port number

"3266"

Class Method Summary (collapse)

Class Method Details

+ (Object) aaseq(arg)

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



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# File 'lib/bio/io/dbget.rb', line 142

def DBGET.aaseq(arg)
  dbget("bget", "-f -n a #{arg}")
end

+ (Object) alink(arg)

alink("db entry") method returns relations



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# File 'lib/bio/io/dbget.rb', line 100

def DBGET.alink(arg)
  dbget("alink", arg)
end

+ (Object) bfind(arg)

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



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# File 'lib/bio/io/dbget.rb', line 105

def DBGET.bfind(arg)
  dbget("bfind", arg)
end

+ (Object) bget(arg)

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



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# File 'lib/bio/io/dbget.rb', line 110

def DBGET.bget(arg)
  dbget("bget", arg)
end

+ (Object) binfo(arg)

binfo("db") method retrieves the database information



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# File 'lib/bio/io/dbget.rb', line 147

def DBGET.binfo(arg)
  dbget("binfo", arg)
end

+ (Object) blink(arg)

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



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# File 'lib/bio/io/dbget.rb', line 152

def DBGET.blink(arg)
  dbget("blink", arg)
end

+ (Object) bman(arg)

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



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# File 'lib/bio/io/dbget.rb', line 157

def DBGET.bman(arg)
  dbget("bman", arg)
end

+ (Object) bref(arg)

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



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# File 'lib/bio/io/dbget.rb', line 162

def DBGET.bref(arg)
  dbget("bref", arg)
end

+ (Object) btab(arg)

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



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# File 'lib/bio/io/dbget.rb', line 167

def DBGET.btab(arg)
  dbget("btab", arg)
end

+ (Object) btit(arg)

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



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# File 'lib/bio/io/dbget.rb', line 172

def DBGET.btit(arg)
  dbget("btit", arg)
end

+ (Object) 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/.



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# 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

+ (Object) naseq(arg)

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



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# File 'lib/bio/io/dbget.rb', line 136

def DBGET.naseq(arg)
  dbget("bget", "-f -n n #{arg}")
end

+ (Object) 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.



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# File 'lib/bio/io/dbget.rb', line 119

def DBGET.seq(arg)
  dbget("bget", "-f -n 1 #{arg}")
end

+ (Object) 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.



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# File 'lib/bio/io/dbget.rb', line 130

def DBGET.seq2(arg)
  dbget("bget", "-f -n 2 #{arg}")
end

+ (Object) version

Show the version information of the DBGET server.



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# File 'lib/bio/io/dbget.rb', line 88

def DBGET.version
  dbget("bget", "-V")
end