bio 1.4.2 → 1.4.3

data/doc/RELEASE_NOTES-1.4.2.rdoc

@@ -0,0 +1,132 @@
+= BioRuby 1.4.2 RELEASE NOTES
+
+A lot of changes have been made to the BioRuby 1.4.2 after the version 1.4.1
+is released. This document describes important and/or incompatible changes
+since the BioRuby 1.4.1 release.
+
+For known problems, see KNOWN_ISSUES.rdoc.
+
+== New features
+
+=== Speed-up of Bio::RestrictionEnzyme::Analysis.cut
+
+The running speed of Bio::RestrictionEnzyme::Analysis.cut is significantly
+increased. The new code is 50 to 80 fold faster than the previous code
+when cutting 1Mbp sequence running on Ruby 1.9.2p180. The code is written
+by Tomoaki NISHIYAMA and Naohisa Goto.
+
+=== New classes Bio::DDBJ::REST, REST interface for DDBJ web service
+
+For DDBJ Web API for Biology (WABI) web service, in additon to SOAP, REST
+(REpresentational State Transfer) interface is added as Bio::DDBJ::REST.
+Currently, only selected APIs are implemented.
+
+=== Bio::Blast with remote DDBJ server uses REST instead of SOAP
+
+Bio::Blast with remote DDBJ server uses REST instead of SOAP, because
+Soap4r (SOAP library for Ruby) does not work well with Ruby 1.9.
+We can now use remote DDBJ BLAST server with Ruby 1.9.
+
+=== Tutorial is updated
+
+The Tutorial.rd is updated by Pjotr Prins and Michael O'Keefe.
+
+=== Many unit tests are added
+
+Added many unit tests for Bio::GenBank, Bio::GenPept, Bio::NBRF, Bio::PDB
+and so on. Most of them are developed by Kazuhiro Hayashi during the
+Google Summer of Code 2010.
+
+=== Other new features
+
+* New method Bio::Fastq#to_s for convenience. Note that the use of the method
+  may cause loss of performance. To get each input sequence entry as-is,
+  consider using Bio::FlatFile#entry_raw. To output fastq format data,
+  consider using Bio::Sequence#output(:fastq).
+* New methods Bio::NCBI::REST::EFetch.nucleotide and protein,
+  to get data from "nucleotide" and "protein" database respectively.
+  Because NCBI changed not to accept "gb" format for the database
+  "sequence", the two new methods are added for convenience.
+* In BioRuby Shell, efetch method uses the above new methods.
+* In GenomeNet remote BLAST execution, database "mine-aa" and "mine-nt"
+  with KEGG organism codes are now supported.
+* Support for Ruby 1.9.2 / 1.9.3 is improved.
+
+== Bug fixes
+
+=== Bio::Blast
+
+* Failure of remote BLAST execution is fixed, due to the changes in GenomeNet
+  and DDBJ.
+* When executing remote BLAST with "genomenet" server, options "-b" and "-v"
+  are now correctly used to limit the number of hits to be reported.
+
+=== Bio::SPTR (Bio::UniProt)
+
+* Due to the UniProtKB format changes, ID, DE, and WEB RESOURCE of CC lines
+  were not correctly parsed. See also below about incompatible change of
+  the fix.
+
+=== Other bug fixes
+
+* Bio::Reference#pubmed_url is updated to follow recent NCBI changes.
+* Fixed: Bio::Newick#reparse failure.
+* Fixed: In Bio::MEDLINE#reference, doi field should be filled.
+* Fixed: Bio::Reference#endnote fails when url is not set.
+* Fixed: Bio::FastaFormat#query passes nil to the given factory object.
+* Fixed: In BioRuby Shell, efetch() with no additional arguments fails
+  because of the NCBI site changes.
+* Fixed: In BioRuby Shell, getent() fails when EMBOSS seqret is not found.
+* Fixed: In BioRuby Shell, demo() fails due to the above two issues.
+
+== Incompatible changes
+
+=== Bio::Sequence#output(:fastq)
+
+In Fastq output formatter, default width value is changed from 70 to nil.
+The nil means "without wrapping". The new default behavior without wrapping
+is generally good with many recent applications that read fastq.
+
+=== Bio::SPTR CC line topic "WEB RESOURCE"
+
+In the return value of Bio::SPTR#cc('WEB RESOURCE'), "NAME" and "NOTE"
+are now renamed to "Name" and "Note", respectively. The change is due to
+the UniProt format change since UniProtKB release 12.2 of 11-Sep-2007.
+(See http://www.uniprot.org/docs/sp_news.htm#rel12.2 for details.)
+Note that "Name" and "Note" are used even when parsing older format.
+The change would also affect Marshal.dump (and YAML.dump) data.
+
+=== Bio::Blast with the remote GenomeNet server
+
+When executing remote BLAST with "genomenet" server, options "-b" and "-v"
+are now correctly used to limit the number of hits to be reported.
+In 1.4.1 and before, "-B" and "-V" were mistakenly used for the purpose.
+
+=== Bio::Blast with the remote DDBJ server
+
+Bio::Blast with remote DDBJ server uses REST instead of SOAP.
+
+=== Bio::RestrictionEnzyme internal data structure change
+
+Due to the speedup, internal data structure of the following classes
+are changed: Bio::RestrictionEnzyme::Range::SequenceRange,
+Bio::RestrictionEnzyme::Range::SequenceRange::CalculatedCuts,
+Bio::RestrictionEnzyme::Range::SequenceRange::Fragment.
+This indicates that Marshal.dump (and YAML.dump) data generated by older
+versions cannot be loaded by the new version, and vice versa, although
+public APIs of the classes keep compatibility.
+
+== Known issues
+
+The following issues are added or updated. See KNOWN_ISSUES.rdoc for other
+already known issues.
+
+* Bio::SPTR should be updated to follow UniProtKB format changes.
+* Problems observed only with Ruby 1.8.5 or earlier will not be fixed.
+* Descriptions about very old RubyGems 0.8.11 or earlier and about CVS
+  repository are moved from README.rdoc.
+
+== Other important news
+
+* Required ruby version is now Ruby 1.8.6 or later (except 1.9.0).
+

data/doc/Tutorial.rd

@@ -40,7 +40,7 @@ bioruby> $: << '../lib'  # make sure rubydoctest finds bioruby/lib
 * Copyright (C) 2001-2003 KATAYAMA Toshiaki <k .at. bioruby.org>
 * Copyright (C) 2005-2011 Pjotr Prins, Naohisa Goto and others
 
-This document was last modified: 2011/03/24
+This document was last modified: 2011/10/14
 Current editor: Michael O'Keefe <okeefm (at) rpi (dot) edu>
 
 The latest version resides in the GIT source code repository:  ./doc/((<Tutorial.rd|URL:https://github.com/bioruby/bioruby/blob/master/doc/Tutorial.rd>)).
@@ -62,7 +62,7 @@ version it has with the
 
 command. You should see something like:
 
-  ruby 1.8.7 (2008-08-11 patchlevel 72) [i486-linux]
+  ruby 1.9.2p290 (2011-07-09 revision 32553) [i686-linux]
 
 If you see no such thing you'll have to install Ruby using your installation
 manager. For more information see the
@@ -1394,6 +1394,22 @@ For a tutorial see ((<here|URL:http://rtags.rubyforge.org/>))
 
 = APPENDIX
 
+== Biogem: Additional BioRuby plugins
+
+Biogem is one of the exciting developments for Ruby in bioinformatics! Biogems
+add new functionality next to the BioRuby core project (BioRuby is a biogem itself). A biogem is simply installed with 
+
+  gem install bio                 # The core BioRuby gem
+  gem install bio-core            # BioRuby + stable pure Ruby biogems
+  gem install bio-core-ext        # bio-core + stable Ruby extensions
+
+Information on these biogems, and the many others available, see ((<Biogems.info|URL:http://biogems.info/>)) or ((<gems.bioruby.org|URL:http://gems.bioruby.org/>)).
+
+
+
+
+
+
 == KEGG API
 
 Please refer to KEGG_API.rd.ja (English version: ((<URL:http://www.genome.jp/kegg/soap/doc/keggapi_manual.html>)) ) and
@@ -1430,7 +1446,9 @@ homologues.
 
 == Using BioPerl or BioPython from Ruby
 
-At the moment there is no easy way of accessing BioPerl from Ruby. The best way, perhaps, is to create a Perl server that gets accessed through XML/RPC or SOAP.
+A possible route is to opt for JRuby and Jython on the JAVA virtual machine (JVM).
+
+At the moment there is no easy way of accessing BioPerl or BioPython directly from Ruby. A possibility is to create a Perl or Python server that gets accessed through XML/RPC or SOAP.
 
 == Installing required external libraries
 

data/doc/Tutorial.rd.html

@@ -4,7 +4,7 @@
   "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
 <html xmlns="http://www.w3.org/1999/xhtml">
 <head>
-<title>doc/Tutorial.rd</title>
+<title>Tutorial.rd</title>
 <link href="bioruby.css" type="text/css" rel="stylesheet" />
 </head>
 <body>
@@ -13,7 +13,7 @@
 <li>Copyright (C) 2001-2003 KATAYAMA Toshiaki &lt;k .at. bioruby.org&gt;</li>
 <li>Copyright (C) 2005-2011 Pjotr Prins, Naohisa Goto and others</li>
 </ul>
-<p>This document was last modified: 2011/03/24
+<p>This document was last modified: 2011/10/14
 Current editor: Michael O'Keefe &lt;okeefm (at) rpi (dot) edu&gt;</p>
 <p>The latest version resides in the GIT source code repository:  ./doc/<a href="https://github.com/bioruby/bioruby/blob/master/doc/Tutorial.rd">Tutorial.rd</a>.</p>
 <h2><a name="label-1" id="label-1">Introduction</a></h2><!-- RDLabel: "Introduction" -->
@@ -27,7 +27,7 @@ by Dave Thomas and Andy Hunt - the first edition can be read online
 version it has with the</p>
 <pre>% ruby -v</pre>
 <p>command. You should see something like:</p>
-<pre>ruby 1.8.7 (2008-08-11 patchlevel 72) [i486-linux]</pre>
+<pre>ruby 1.9.2p290 (2011-07-09 revision 32553) [i686-linux]</pre>
 <p>If you see no such thing you'll have to install Ruby using your installation
 manager. For more information see the
 <a href="http://www.ruby-lang.org/en/">Ruby</a> website.</p>
@@ -1119,17 +1119,24 @@ source code by clicking on class and method names. </p>
 rtags -R --vi</pre>
 <p>For a tutorial see <a href="http://rtags.rubyforge.org/">here</a></p>
 <h1><a name="label-34" id="label-34">APPENDIX</a></h1><!-- RDLabel: "APPENDIX" -->
-<h2><a name="label-35" id="label-35">KEGG API</a></h2><!-- RDLabel: "KEGG API" -->
+<h2><a name="label-35" id="label-35">Biogem: Additional BioRuby plugins</a></h2><!-- RDLabel: "Biogem: Additional BioRuby plugins" -->
+<p>Biogem is one of the exciting developments for Ruby in bioinformatics! Biogems
+add new functionality next to the BioRuby core project (BioRuby is a biogem itself). A biogem is simply installed with </p>
+<pre>gem install bio                 # The core BioRuby gem
+gem install bio-core            # BioRuby + stable pure Ruby biogems
+gem install bio-core-ext        # bio-core + stable Ruby extensions</pre>
+<p>Information on these biogems, and the many others available, see <a href="http://biogems.info/">Biogems.info</a> or <a href="http://gems.bioruby.org/">gems.bioruby.org</a>.</p>
+<h2><a name="label-36" id="label-36">KEGG API</a></h2><!-- RDLabel: "KEGG API" -->
 <p>Please refer to KEGG_API.rd.ja (English version: <a href="http://www.genome.jp/kegg/soap/doc/keggapi_manual.html">&lt;URL:http://www.genome.jp/kegg/soap/doc/keggapi_manual.html&gt;</a> ) and</p>
 <ul>
 <li><a href="http://www.genome.jp/kegg/soap/">&lt;URL:http://www.genome.jp/kegg/soap/&gt;</a></li>
 </ul>
-<h2><a name="label-36" id="label-36">Ruby Ensembl API</a></h2><!-- RDLabel: "Ruby Ensembl API" -->
+<h2><a name="label-37" id="label-37">Ruby Ensembl API</a></h2><!-- RDLabel: "Ruby Ensembl API" -->
 <p>The Ruby Ensembl API is a Ruby API to the Ensembl database. It is NOT currently
 included in the BioRuby archives. To install it, see
 <a href="http://wiki.github.com/jandot/ruby-ensembl-api">the Ruby-Ensembl Github</a>
 for more information.</p>
-<h3><a name="label-37" id="label-37">Gene Ontology (GO) through the Ruby Ensembl API</a></h3><!-- RDLabel: "Gene Ontology (GO) through the Ruby Ensembl API" -->
+<h3><a name="label-38" id="label-38">Gene Ontology (GO) through the Ruby Ensembl API</a></h3><!-- RDLabel: "Gene Ontology (GO) through the Ruby Ensembl API" -->
 <p>Gene Ontologies can be fetched through the Ruby Ensembl API package:</p>
 <pre>require 'ensembl'
 Ensembl::Core::DBConnection.connect('drosophila_melanogaster')
@@ -1146,9 +1153,10 @@ infile.each do |line|
 end</pre>
 <p>Prints each mosq. accession/uniq identifier and the GO terms from the Drosphila
 homologues.</p>
-<h2><a name="label-38" id="label-38">Using BioPerl or BioPython from Ruby</a></h2><!-- RDLabel: "Using BioPerl or BioPython from Ruby" -->
-<p>At the moment there is no easy way of accessing BioPerl from Ruby. The best way, perhaps, is to create a Perl server that gets accessed through XML/RPC or SOAP.</p>
-<h2><a name="label-39" id="label-39">Installing required external libraries</a></h2><!-- RDLabel: "Installing required external libraries" -->
+<h2><a name="label-39" id="label-39">Using BioPerl or BioPython from Ruby</a></h2><!-- RDLabel: "Using BioPerl or BioPython from Ruby" -->
+<p>A possible route is to opt for JRuby and Jython on the JAVA virtual machine (JVM).</p>
+<p>At the moment there is no easy way of accessing BioPerl or BioPython directly from Ruby. A possibility is to create a Perl or Python server that gets accessed through XML/RPC or SOAP.</p>
+<h2><a name="label-40" id="label-40">Installing required external libraries</a></h2><!-- RDLabel: "Installing required external libraries" -->
 <p>At this point for using BioRuby no additional libraries are needed, except if
 you are using the Bio::PhyloXML module; then you have to install libxml-ruby.</p>
 <p>This may change, so keep an eye on the Bioruby website. Also when
@@ -1157,20 +1165,20 @@ a package is missing BioRuby should show an informative message.</p>
 painful, as the gem standard for packages evolved late and some still
 force you to copy things by hand. Therefore read the README's
 carefully that come with each package.</p>
-<h3><a name="label-40" id="label-40">Installing libxml-ruby</a></h3><!-- RDLabel: "Installing libxml-ruby" -->
+<h3><a name="label-41" id="label-41">Installing libxml-ruby</a></h3><!-- RDLabel: "Installing libxml-ruby" -->
 <p>The simplest way is to use the RubyGems packaging system:</p>
 <pre>gem install -r libxml-ruby</pre>
 <p>If you get `require': no such file to load - mkmf (LoadError) error then do</p>
 <pre>sudo apt-get install ruby-dev</pre>
 <p>If you have other problems with installation, then see <a href="http://libxml.rubyforge.org/install.xml">&lt;URL:http://libxml.rubyforge.org/install.xml&gt;</a>.</p>
-<h2><a name="label-41" id="label-41">Trouble shooting</a></h2><!-- RDLabel: "Trouble shooting" -->
+<h2><a name="label-42" id="label-42">Trouble shooting</a></h2><!-- RDLabel: "Trouble shooting" -->
 <ul>
 <li>Error: in `require': no such file to load -- bio (LoadError)</li>
 </ul>
 <p>Ruby is failing to find the BioRuby libraries - add it to the RUBYLIB path, or pass
 it to the interpeter. For example:</p>
 <pre>ruby -I$BIORUBYPATH/lib yourprogram.rb</pre>
-<h2><a name="label-42" id="label-42">Modifying this page</a></h2><!-- RDLabel: "Modifying this page" -->
+<h2><a name="label-43" id="label-43">Modifying this page</a></h2><!-- RDLabel: "Modifying this page" -->
 <p>IMPORTANT NOTICE: This page is maintained in the BioRuby source code 
 repository. Please edit the file there otherwise changes may get
 lost. See <!-- Reference, RDLabel "BioRuby Developer Information" doesn't exist --><em class="label-not-found">BioRuby Developer Information</em><!-- Reference end --> for repository and mailing list

data/etc/bioinformatics/seqdatabase.ini

@@ -2,209 +2,26 @@ VERSION=1.00
 
 [embl]
 protocol=biofetch
-location=http://bioruby.org/cgi-bin/biofetch.rb
+location=http://www.ebi.ac.uk/Tools/dbfetch/dbfetch
 dbname=embl
 
-[embl-upd]
+[emblcds]
 protocol=biofetch
-location=http://bioruby.org/cgi-bin/biofetch.rb
-dbname=embl-upd
+location=http://www.ebi.ac.uk/Tools/dbfetch/dbfetch
+dbname=emblcds
 
-[embl_biofetch]
+[uniprotkb]
 protocol=biofetch
-location=http://www.ebi.ac.uk/cgi-bin/dbfetch
-dbname=embl
-
-[embl_biosql]
-protocol=biosql
-location=localhost
-dbname=biosql
-driver=postgres
-user=hack 
-pass=
-biodbname=embl
-
-[embl_biocorba]
-protocol=bsane-corba
-location=sqldbsrv.ior
-
-[embl_xembl]
-protocol=xembl
-location=http://www.ebi.ac.uk/xembl/XEMBL.wsdl
-format=Bsml
-
-[embl_flat]
-protcol=flat
-location=/export/database/
-dbname=embl
-
-[genbank_bdb]
-protcol=flat
-location=/export/database/
-dbname=genbank
-
-[swissprot]
-protocol=biofetch
-location=http://bioruby.org/cgi-bin/biofetch.rb
-dbname=swissprot
-
-[swissprot-upd]
-protocol=biofetch
-location=http://bioruby.org/cgi-bin/biofetch.rb
-dbname=swissprot-upd
-
-[swissprot_biofetch]
-protocol=biofetch
-location=http://www.ebi.ac.uk/cgi-bin/dbfetch
-dbname=swall
-
-[swissprot_biosql]
-protocol=biosql
-location=db.bioruby.org
-dbname=biosql
-driver=mysql
-user=root
-pass= 
-biodbname=sp
-
-
-[genbank]
-protocol=biofetch
-location=http://bioruby.org/cgi-bin/biofetch.rb
-dbname=genbank
-
-[genbank-upd]
-protocol=biofetch
-location=http://bioruby.org/cgi-bin/biofetch.rb
-dbname=genbank-upd
-
-[genbank_biosql]
-protocol=biosql
-location=db.bioruby.org
-dbname=biosql
-driver=mysql
-user=root
-pass= 
-biodbname=gb
-
-
-[refseq]
-protocol=biofetch
-location=http://bioruby.org/cgi-bin/biofetch.rb
-dbname=refseq
-
-[refseq_biosql]
-protocol=biosql
-location=db.bioruby.org
-dbname=biosql
-driver=mysql
-user=
-pass= 
-biodbname=rs
-
-
-[kegg-pathway]
-protocol=biofetch
-location=http://bioruby.org/cgi-bin/biofetch.rb
-dbname=pathway
-
-[kegg-genome]
-protocol=biofetch
-location=http://bioruby.org/cgi-bin/biofetch.rb
-dbname=genome
-
-[kegg-genes]
-protocol=biofetch
-location=http://bioruby.org/cgi-bin/biofetch.rb
-dbname=genes
-
-[kegg-vgenes]
-protocol=biofetch
-location=http://bioruby.org/cgi-bin/biofetch.rb
-dbname=vgenes
-
-[aaindex]
-protocol=biofetch
-location=http://bioruby.org/cgi-bin/biofetch.rb
-dbname=aaindex
-
-[blocks]
-protocol=biofetch
-location=http://bioruby.org/cgi-bin/biofetch.rb
-dbname=blocks
-
-[enzyme]
-protocol=biofetch
-location=http://bioruby.org/cgi-bin/biofetch.rb
-dbname=enzyme
-
-[epd]
-protocol=biofetch
-location=http://bioruby.org/cgi-bin/biofetch.rb
-dbname=epd
-
-[litdb]
-protocol=biofetch
-location=http://bioruby.org/cgi-bin/biofetch.rb
-dbname=litdb
-
-[omim]
-protocol=biofetch
-location=http://bioruby.org/cgi-bin/biofetch.rb
-dbname=omim
-
-[pdb]
-protocol=biofetch
-location=http://bioruby.org/cgi-bin/biofetch.rb
-dbname=pdb
-
-[pdbstr]
-protocol=biofetch
-location=http://bioruby.org/cgi-bin/biofetch.rb
-dbname=pdbstr
-
-[pfam]
-protocol=biofetch
-location=http://bioruby.org/cgi-bin/biofetch.rb
-dbname=pfam
-
-[pir]
-protocol=biofetch
-location=http://bioruby.org/cgi-bin/biofetch.rb
-dbname=pir
-
-[pmd]
-protocol=biofetch
-location=http://bioruby.org/cgi-bin/biofetch.rb
-dbname=pmd
-
-[prf]
-protocol=biofetch
-location=http://bioruby.org/cgi-bin/biofetch.rb
-dbname=prf
-
-[prints]
-protocol=biofetch
-location=http://bioruby.org/cgi-bin/biofetch.rb
-dbname=prints
-
-[prodom]
-protocol=biofetch
-location=http://bioruby.org/cgi-bin/biofetch.rb
-dbname=prodom
-
-[prosdoc]
-protocol=biofetch
-location=http://bioruby.org/cgi-bin/biofetch.rb
-dbname=prosdoc
+location=http://www.ebi.ac.uk/Tools/dbfetch/dbfetch
+dbname=uniprotkb
 
-[prosite]
+[refseqn]
 protocol=biofetch
-location=http://bioruby.org/cgi-bin/biofetch.rb
-dbname=prosite
+location=http://www.ebi.ac.uk/Tools/dbfetch/dbfetch
+dbname=refseqn
 
-[transfac]
+[refseqp]
 protocol=biofetch
-location=http://bioruby.org/cgi-bin/biofetch.rb
-dbname=transfac
+location=http://www.ebi.ac.uk/Tools/dbfetch/dbfetch
+dbname=refseqp