class Bio::DBGET
Constants
Public Class Methods
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(“db entry”) method returns relations
# File lib/bio/io/dbget.rb, line 100 def DBGET.alink(arg) dbget("alink", arg) end
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(“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(“db”) method retrieves the database information
# File lib/bio/io/dbget.rb, line 147 def DBGET.binfo(arg) dbget("binfo", arg) end
blink(“db entry”) method retrieves the link information
# File lib/bio/io/dbget.rb, line 152 def DBGET.blink(arg) dbget("blink", arg) end
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(“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 (“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(“db entry ..”) method retrieves the entry definition
# File lib/bio/io/dbget.rb, line 172 def DBGET.btit(arg) dbget("btit", arg) end
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 ::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(“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(“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 ::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(“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 ::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
Show the version information of the DBGET server.
# File lib/bio/io/dbget.rb, line 88 def DBGET.version dbget("bget", "-V") end