From k at pub.open-bio.org Mon Jul 11 05:30:48 2005 From: k at pub.open-bio.org (Katayama Toshiaki) Date: Mon Jul 11 06:20:32 2005 Subject: [BioRuby-cvs] bioruby/lib/bio/io higet.rb{sVv} Message-ID: <200507110930.j6B9UmdZ009746@pub.open-bio.org> Update of /home/repository/bioruby/bioruby/lib/bio/io In directory pub.open-bio.org:/tmp/cvs-serv9742/lib/bio/io Added Files: higet.rb Log Message: * Newly added SOAP interface for HGC HiGet service --- NEW FILE: higet.rb --- # # bio/io/higet.rb - SOAP interface for HGC HiGet # # Copyright (C) 2005 KATAYAMA Toshiaki # # This library is free software; you can redistribute it and/or # modify it under the terms of the GNU Lesser General Public # License as published by the Free Software Foundation; either # version 2 of the License, or (at your option) any later version. # # This library is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU # Lesser General Public License for more details. # # You should have received a copy of the GNU Lesser General Public # License along with this library; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA # # $Id: higet.rb,v 1.1 2005/07/11 09:30:46 k Exp $ # require 'bio/io/soapwsdl' module Bio class HGC class HiGet < Bio::SOAPWSDL SERVER_URI = "http://higet.hgc.jp/soap/higet.wsdl" def initialize(wsdl = nil) super(wsdl || SERVER_URI) end def higet_in_fasta(db, entries) self.higet(db, entries, "-d fasta") end def higet_in_xml(db, entries) self.higet(db, entries, "-d xml") end end end # HGC end # Bio if __FILE__ == $0 begin require 'pp' alias :p :pp rescue LoadError end puts ">>> Bio::HGC::HiGet" serv = Bio::HGC::HiGet.new serv.log = STDERR puts "### HiFind" puts serv.hifind("genbank", "human kinase", "-l 10") puts "### HiGet" puts serv.higet("genbank", "S40289", "") puts "### HiGet (FASTA)" puts serv.higet("genbank", "S40289", "-d fasta") puts "### HiGet higet_in_fasta" puts serv.higet_in_fasta("genbank", "S40289") puts "### HiGet higet_in_xml" puts serv.higet_in_xml("genbank", "S40289") end =begin = Bio::HGC::HiGet * (()) == HiGet#hifind == HiGet#higet == HiGet#higet_in_fasta == HiGet#higet_in_xml =end From k at pub.open-bio.org Mon Jul 11 05:31:34 2005 From: k at pub.open-bio.org (Katayama Toshiaki) Date: Mon Jul 11 06:21:12 2005 Subject: [BioRuby-cvs] bioruby/bin br_pmfetch.rb{sVv} Message-ID: <200507110931.j6B9VYdZ009794@pub.open-bio.org> Update of /home/repository/bioruby/bioruby/bin In directory pub.open-bio.org:/tmp/cvs-serv9790/bin Modified Files: br_pmfetch.rb Log Message: * --sort page option is now available Index: br_pmfetch.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/bin/br_pmfetch.rb,v retrieving revision 1.4 retrieving revision 1.5 diff -C2 -d -r1.4 -r1.5 *** br_pmfetch.rb 6 Jan 2005 12:28:16 -0000 1.4 --- br_pmfetch.rb 11 Jul 2005 09:31:32 -0000 1.5 *************** *** 168,172 **** Sort: ! author, journal, pub+date See the following pages for the PubMed search options: --- 168,172 ---- Sort: ! author, journal, pub+date, page See the following pages for the PubMed search options: *************** *** 248,251 **** --- 248,254 ---- when /--version/ raise PMFetch::Version + when /--sort/ + @sort = optarg + @search_opts["sort"] = @sort unless @sort == "page" else optname.delete!('-') *************** *** 285,290 **** else entries = parse_entries(entries) ! if @format == 'report' entries = sort_entries(entries) report_format(entries) else --- 288,295 ---- else entries = parse_entries(entries) ! if @sort == 'page' entries = sort_entries(entries) + end + if @format == 'report' report_format(entries) else *************** *** 311,319 **** if RUBY_VERSION > "1.8.0" entries.sort_by { |x| ! [ x.journal, x.volume, x.issue, x.pages.to_i ] } else entries.map { |x| ! [ x.journal, x.volume, x.issue, x.pages.to_i, x ] }.sort { |a, b| a[0..3] <=> b[0..3] --- 316,324 ---- if RUBY_VERSION > "1.8.0" entries.sort_by { |x| ! [ x.journal, x.volume.to_i, x.issue.to_i, x.pages.to_i ] } else entries.map { |x| ! [ x.journal, x.volume.to_i, x.issue.to_i, x.pages.to_i, x ] }.sort { |a, b| a[0..3] <=> b[0..3] *************** *** 348,352 **** = Examples : PubMed search ! These for lines will do the same job. % PMFetch transcription factor --- 353,357 ---- = Examples : PubMed search ! These four lines will do the same job. % PMFetch transcription factor From k at pub.open-bio.org Mon Jul 11 05:37:00 2005 From: k at pub.open-bio.org (Katayama Toshiaki) Date: Mon Jul 11 06:25:40 2005 Subject: [BioRuby-cvs] CVSROOT loginfo{sVv} Message-ID: <200507110937.j6B9b0dZ009836@pub.open-bio.org> Update of /home/repository/bioruby/CVSROOT In directory pub.open-bio.org:/tmp/cvs-serv9832 Modified Files: loginfo Log Message: * fixed mail subject, hopefully Index: loginfo =================================================================== RCS file: /home/repository/bioruby/CVSROOT/loginfo,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -d -r1.3 -r1.4 *** loginfo 29 Jun 2005 11:22:25 -0000 1.3 --- loginfo 11 Jul 2005 09:36:58 -0000 1.4 *************** *** 26,28 **** # or #DEFAULT (echo ""; id; echo %{sVv}; date; cat) >> $CVSROOT/CVSROOT/commitlog ! DEFAULT /usr/local/bin/syncmail %s{sVv} bioruby-cvs@portal.open-bio.org --- 26,28 ---- # or #DEFAULT (echo ""; id; echo %{sVv}; date; cat) >> $CVSROOT/CVSROOT/commitlog ! DEFAULT /usr/local/bin/syncmail %{sVv} bioruby-cvs@portal.open-bio.org From k at pub.open-bio.org Mon Jul 11 05:37:35 2005 From: k at pub.open-bio.org (Katayama Toshiaki) Date: Mon Jul 11 06:26:16 2005 Subject: [BioRuby-cvs] bioruby ChangeLog,1.26,1.27 Message-ID: <200507110937.j6B9bZdZ009863@pub.open-bio.org> Update of /home/repository/bioruby/bioruby In directory pub.open-bio.org:/tmp/cvs-serv9859 Modified Files: ChangeLog Log Message: * added higet Index: ChangeLog =================================================================== RCS file: /home/repository/bioruby/bioruby/ChangeLog,v retrieving revision 1.26 retrieving revision 1.27 diff -C2 -d -r1.26 -r1.27 *** ChangeLog 29 Jun 2005 11:24:28 -0000 1.26 --- ChangeLog 11 Jul 2005 09:37:33 -0000 1.27 *************** *** 1,2 **** --- 1,11 ---- + 2005-07-11 Toshiaki Katayama + + * bin/br_pmfetch.rb + * added sort by page option (--sort page) + + * lib/io/higet.rb + + Newly added Bio::HGC::HiGet class for HiGet SOAP service. + 2005-06-28 Toshiaki Katayama *************** *** 9,12 **** --- 18,28 ---- Newly added Bio::GO::External2go class for parsing external2go file. + + 2005-02-09 KATAYAMA Toshiaki + + * lib/bio/db/kegg/genes.rb + + Added cu method which returns codon usage in Hash for the + convenience (codon_usage method returns in Array or Fixnum). 2004-12-13 KATAYAMA Toshiaki From k at pub.open-bio.org Mon Jul 11 05:40:04 2005 From: k at pub.open-bio.org (Katayama Toshiaki) Date: Mon Jul 11 06:29:19 2005 Subject: [BioRuby-cvs] bioruby/lib bio.rb,1.41,1.42 Message-ID: <200507110940.j6B9e4dZ009928@pub.open-bio.org> Update of /home/repository/bioruby/bioruby/lib In directory pub.open-bio.org:/tmp/cvs-serv9919/lib Modified Files: bio.rb Log Message: * added higet * prepared for 0.6.3 Index: bio.rb =================================================================== RCS file: /home/repository/bioruby/bioruby/lib/bio.rb,v retrieving revision 1.41 retrieving revision 1.42 diff -C2 -d -r1.41 -r1.42 *** bio.rb 13 Dec 2004 05:17:48 -0000 1.41 --- bio.rb 11 Jul 2005 09:40:02 -0000 1.42 *************** *** 2,6 **** # bio.rb - Loading all BioRuby modules # ! # Copyright (C) 2001-2004 KATAYAMA Toshiaki # # This library is free software; you can redistribute it and/or --- 2,6 ---- # bio.rb - Loading all BioRuby modules # ! # Copyright (C) 2001-2005 KATAYAMA Toshiaki # # This library is free software; you can redistribute it and/or *************** *** 22,26 **** module Bio ! BIORUBY_VERSION = [0, 6, 2].extend(Comparable) end --- 22,26 ---- module Bio ! BIORUBY_VERSION = [0, 6, 3].extend(Comparable) end *************** *** 116,119 **** --- 116,120 ---- require 'bio/io/das' require 'bio/io/ddbjxml' + require 'bio/io/higet' #require 'bio/io/esoap' #require 'bio/io/brdb'