[BioRuby-cvs] bioruby/lib/bio/io dbget.rb,1.10,1.11
Katayama Toshiaki
k at pub.open-bio.org
Sat Nov 5 03:32:28 EST 2005
Update of /home/repository/bioruby/bioruby/lib/bio/io
In directory pub.open-bio.org:/tmp/cvs-serv29757/lib/bio/io
Modified Files:
dbget.rb
Log Message:
* converted to RDoc
Index: dbget.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/io/dbget.rb,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** dbget.rb 8 Sep 2005 01:22:11 -0000 1.10
--- dbget.rb 5 Nov 2005 08:32:26 -0000 1.11
***************
*** 1,7 ****
#
! # bio/io/dbget.rb - GenomeNet/DBGET client module
#
! # Copyright (C) 2000 Mitsuteru C. Nakao <n at bioruby.org>
! # Copyright (C) 2000, 2001 KATAYAMA Toshiaki <k at bioruby.org>
#
# This library is free software; you can redistribute it and/or
--- 1,18 ----
#
! # = bio/io/dbget.rb - GenomeNet/DBGET client module
#
! # Copyright:: Copyright (C) 2000, 2001
! # Mitsuteru C. Nakao <n at bioruby.org>,
! # Toshiaki Katayama <k at bioruby.org>
! # License:: LGPL
! #
! # $Id$
! #
! # == DBGET
! #
! # Accessing the GenomeNet/DBGET data retrieval system
! # http://www.genome.jp/dbget/ within the intranet.
! #
! #--
#
# This library is free software; you can redistribute it and/or
***************
*** 19,23 ****
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
! # $Id$
#
--- 30,34 ----
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
! #++
#
***************
*** 26,135 ****
module Bio
! class DBGET
! # SERV = "dbgetserv.genome.jp" # default DBGET server address
! SERV = "dbget.genome.jp" # default DBGET server address
! PORT = "3266" # default DBGET port number
! 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
! def DBGET.version
! dbget("bget", "-V")
! end
! ### Individual DBGET functions (in alphabetical order)
! # alink("db entry") - print relations
! def DBGET.alink(arg)
! dbget("alink", arg)
! end
! # bacc("db entry") - not supported : get accession(s)
! # bent("db entry") - not supported : get entry name
! # bfind("db keyword") - search entries by keyword
! def DBGET.bfind(arg)
! dbget("bfind", arg)
! end
! # bget("db entry") - get entry by the entry name
! def DBGET.bget(arg)
! dbget("bget", arg)
! end
! def DBGET.seq(arg)
! dbget("bget", "-f -n 1 #{arg}")
! end
! def DBGET.seq2(arg)
! dbget("bget", "-f -n 2 #{arg}")
! end
! # binfo("db") - get database information
! def DBGET.binfo(arg)
! dbget("binfo", arg)
! end
! # blink("db entry") - print link informations
! def DBGET.blink(arg)
! dbget("blink", arg)
! end
! # bman ("db entry") - print manual page
! def DBGET.bman(arg)
! dbget("bman", arg)
! end
! # bref("db entry") - get references and authors
! def DBGET.bref(arg)
! dbget("bref", arg)
! end
! # btab ("db entry") - get/generate database alias table
! def DBGET.btab(arg)
! dbget("btab", arg)
! end
! # btit("db entry ..") - get entry definition
! def DBGET.btit(arg)
! dbget("btit", arg)
! end
! # lmarge("db entry") - not supported
end
end
if __FILE__ == $0
--- 37,199 ----
module Bio
! class DBGET
! # default DBGET server address
! # SERV = "dbgetserv.genome.jp"
! SERV = "dbget.genome.jp"
! # default DBGET port number
! PORT = "3266"
! # 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 http://www.genome.jp/dbget/.
! #
! 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
! # Show the version information of the DBGET server.
! def DBGET.version
! dbget("bget", "-V")
! end
! #--
! # bacc("db entry") - not supported : get accession(s)
! # bent("db entry") - not supported : get entry name
! # lmarge("db entry") - not supported
! #++
! # alink("db entry") method returns relations
! def DBGET.alink(arg)
! dbget("alink", arg)
! end
! # bfind("db keyword") method searches entries by keyword
! def DBGET.bfind(arg)
! dbget("bfind", arg)
! end
! # bget("db entry") method retrieves entries specified by the entry names
! def DBGET.bget(arg)
! dbget("bget", 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.
! 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.
! def DBGET.seq2(arg)
! dbget("bget", "-f -n 2 #{arg}")
! end
! # naseq("db entry") method retrieves the nucleic acid sequence of the
! # entry if any.
! def DBGET.naseq(arg)
! dbget("bget", "-f -n n #{arg}")
! end
! # aaseq("db entry") method retrieves the amino acid sequence of the
! # entry if any.
! def DBGET.aaseq(arg)
! dbget("bget", "-f -n a #{arg}")
! end
! # binfo("db") method retrieves the database information
! def DBGET.binfo(arg)
! dbget("binfo", arg)
! end
! # blink("db entry") method retrieves the link information
! def DBGET.blink(arg)
! dbget("blink", arg)
! end
! # bman ("db entry") method shows the manual page
! def DBGET.bman(arg)
! dbget("bman", arg)
! end
! # bref("db entry") method retrieves the references and authors
! def DBGET.bref(arg)
! dbget("bref", arg)
! end
! # btab ("db entry") method retrives (and generates) the database alias table
! def DBGET.btab(arg)
! dbget("btab", arg)
! end
+ # btit("db entry ..") method retrieves the entry definition
+ def DBGET.btit(arg)
+ dbget("btit", arg)
end
end
+ end # module Bio
+
if __FILE__ == $0
***************
*** 145,213 ****
puts Bio::DBGET.binfo('dbget')
end
-
-
- =begin
-
- = Bio::DBGET
-
- Accessing the GenomeNet/DBGET data retrieval system
- ((<URL:http://www.genome.jp/dbget/>)).
-
- --- Bio::DBGET.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
-
- '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 ((<URL:http://www.genome.jp/dbget/>)).
-
- --- BIO::DBGET.alink(arg)
- --- Bio::DBGET.bfind(arg)
- --- Bio::DBGET.bget(arg)
- --- Bio::DBGET.binfo(arg)
- --- Bio::DBGET.blink(arg)
- --- Bio::DBGET.bman(arg)
- --- Bio::DBGET.bref(arg)
- --- Bio::DBGET.btab(arg)
- --- Bio::DBGET.btit(arg)
-
- These class 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.
-
- --- Bio::DBGET.version
-
- Show the version information of the DBGET server.
-
- --- Bio::DBGET.seq(arg)
-
- 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.
-
- --- Bio::DBGET.seq2(arg)
-
- 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.
-
- =end
--- 209,212 ----
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