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 Bio::DBGET.dbget(com, arg). Most of these methods accept the argument “-h” for help.
‘arg’ should be one of the following formats :
db
specify the database name only for binfo, bman etc.
db:entry
specify the database name and the entry name to retrieve.
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 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(“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
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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