bio 1.3.0 → 1.3.1

data/test/unit/bio/appl/test_blast.rb

@@ -119,7 +119,7 @@ module Bio
        assert(Bio::Blast.local(@program, @db, @option))
      end
 
-     def test_self_local
+     def test_self_remote
        assert(Bio::Blast.remote(@program, @db, @option))
      end
 

data/test/unit/bio/db/biosql/tc_biosql.rb

@@ -0,0 +1,110 @@
+# To change this template, choose Tools | Templates
+# and open the template in the editor.
+
+$:.unshift File.join(File.dirname(__FILE__),'..','lib')
+
+require 'test/unit'
+require 'bio'
+
+module Bio
+  class TestBiosqlIO < Test::Unit::TestCase
+    def setup
+      @connection = Bio::SQL.establish_connection({'development'=>{'hostname'=>'localhost','database'=>"bioseq", 'adapter'=>"jdbcmysql", 'username'=>"febo", 'password'=>nil}},'development')
+      @str_genbank=<<END
+LOCUS       X64011                   756 bp    DNA     linear   BCT 26-SEP-2006
+DEFINITION  Listeria ivanovii sod gene for superoxide dismutase.
+ACCESSION   X64011 S78972
+VERSION     X64011.1  GI:44010
+KEYWORDS    sod gene; superoxide dismutase.
+SOURCE      Listeria ivanovii
+  ORGANISM  Listeria ivanovii
+            Bacteria; Firmicutes; Bacillales; Listeriaceae; Listeria.
+REFERENCE   1
+  AUTHORS   Haas,A. and Goebel,W.
+  TITLE     Cloning of a superoxide dismutase gene from Listeria ivanovii by
+            functional complementation in Escherichia coli and characterization
+            of the gene product
+  JOURNAL   Mol. Gen. Genet. 231 (2), 313-322 (1992)
+   PUBMED   1736100
+REFERENCE   2  (bases 1 to 756)
+  AUTHORS   Kreft,J.
+  TITLE     Direct Submission
+  JOURNAL   Submitted (21-APR-1992) J. Kreft, Institut f. Mikrobiologie,
+            Universitaet Wuerzburg, Biozentrum Am Hubland, 8700 Wuerzburg, FRG
+COMMENT     On Jun 23, 2005 this sequence version replaced gi:244394.
+FEATURES             Location/Qualifiers
+     source          1..756
+                     /organism="Listeria ivanovii"
+                     /mol_type="genomic DNA"
+                     /strain="ATCC 19119"
+                     /db_xref="taxon:1638"
+     gene            95..746
+                     /gene="sod"
+     RBS             95..100
+                     /gene="sod"
+     CDS             109..717
+                     /gene="sod"
+                     /EC_number="1.15.1.1"
+                     /codon_start=1
+                     /transl_table=11
+                     /product="superoxide dismutase"
+                     /protein_id="CAA45406.1"
+                     /db_xref="GI:44011"
+                     /db_xref="GOA:P28763"
+                     /db_xref="InterPro:IPR001189"
+                     /db_xref="UniProtKB/Swiss-Prot:P28763"
+                     /translation="MTYELPKLPYTYDALEPNFDKETMEIHYTKHHNIYVTKLNEAVS
+                     GHAELASKPGEELVANLDSVPEEIRGAVRNHGGGHANHTLFWSSLSPNGGGAPTGNLK
+                     AAIESEFGTFDEFKEKFNAAAAARFGSGWAWLVVNNGKLEIVSTANQDSPLSEGKTPV
+                     LGLDVWEHAYYLKFQNRRPEYIDTFWNVINWDERNKRFDAAK"
+     terminator      723..746
+                     /gene="sod"
+ORIGIN
+        1 cgttatttaa ggtgttacat agttctatgg aaatagggtc tatacctttc gccttacaat
+       61 gtaatttctt ttcacataaa taataaacaa tccgaggagg aatttttaat gacttacgaa
+      121 ttaccaaaat taccttatac ttatgatgct ttggagccga attttgataa agaaacaatg
+      181 gaaattcact atacaaagca ccacaatatt tatgtaacaa aactaaatga agcagtctca
+      241 ggacacgcag aacttgcaag taaacctggg gaagaattag ttgctaatct agatagcgtt
+      301 cctgaagaaa ttcgtggcgc agtacgtaac cacggtggtg gacatgctaa ccatacttta
+      361 ttctggtcta gtcttagccc aaatggtggt ggtgctccaa ctggtaactt aaaagcagca
+      421 atcgaaagcg aattcggcac atttgatgaa ttcaaagaaa aattcaatgc ggcagctgcg
+      481 gctcgttttg gttcaggatg ggcatggcta gtagtgaaca atggtaaact agaaattgtt
+      541 tccactgcta accaagattc tccacttagc gaaggtaaaa ctccagttct tggcttagat
+      601 gtttgggaac atgcttatta tcttaaattc caaaaccgtc gtcctgaata cattgacaca
+      661 ttttggaatg taattaactg ggatgaacga aataaacgct ttgacgcagc aaaataatta
+      721 tcgaaaggct cacttaggtg ggtcttttta tttcta
+//
+END
+    end
+
+    def test_00_connection
+      assert_instance_of(ActiveRecord::ConnectionAdapters::ConnectionPool, @connection)
+    end
+
+    def test_01_input_is_genbank
+      assert_instance_of(Bio::GenBank,Bio::GenBank.new(@str_genbank))
+    end
+
+    def test_02_insert_bioentry
+      @@x = Bio::SQL::Sequence.new(:biosequence=>Bio::GenBank.new(@str_genbank).to_biosequence, :biodatabase=>Bio::SQL::Biodatabase.find(:first))
+      assert_not_nil(@@x)
+    end
+
+    def test_03_input_output
+      bioseq = Bio::SQL.fetch_accession("X64011")
+      assert_not_nil bioseq
+      assert_equal(@str_genbank, bioseq.to_biosequence.output(:genbank))
+    end
+
+    def test_04_bioentry_data_format
+      assert_equal('26-SEP-2006', @@x.date_modified.to_s)
+    end
+
+    def test_05_title
+      assert_equal('Cloning of a superoxide dismutase gene from Listeria ivanovii by functional complementation in Escherichia coli and characterization of the gene product',@@x.references.first.title)
+    end
+    def test_99_delete_bioentry
+      assert_not_nil(@@x.delete)
+    end
+  end
+end

data/test/unit/bio/db/biosql/ts_suite_biosql.rb

@@ -0,0 +1,8 @@
+# To change this template, choose Tools | Templates
+# and open the template in the editor.
+$:.unshift File.dirname(__FILE__)
+
+require 'test/unit' 
+
+# Add your testcases here
+require 'tc_biosql'

data/test/unit/bio/test_feature.rb

@@ -5,7 +5,7 @@
 #              Mitsuteru Nakao <n@bioruby.org>
 # License::    The Ruby License
 #
-#  $Id: test_feature.rb,v 1.5.2.1 2008/05/08 05:38:01 ngoto Exp $
+#  $Id:$
 #
 
 require 'pathname'
@@ -89,25 +89,26 @@ module Bio
     end
   end
 
-  class NullStderr
-    def initialize
-      @log = []
-    end
+  class TestFeatures < Test::Unit::TestCase
 
-    def write(*arg)
-      #p arg
-      @log.push([ :write, *arg ])
-      nil
-    end
+    class NullStderr
+      def initialize
+        @log = []
+      end
 
-    def method_missing(*arg)
-      #p arg
-      @log.push arg
-      nil
-    end
-  end
+      def write(*arg)
+        #p arg
+        @log.push([ :write, *arg ])
+        nil
+      end
+
+      def method_missing(*arg)
+        #p arg
+        @log.push arg
+        nil
+      end
+    end #class NullStderr
 
-  class TestFeatures < Test::Unit::TestCase
     def setup
       # To suppress warning messages, $stderr is replaced by dummy object.
       @stderr_orig = $stderr

data/test/unit/bio/test_reference.rb

@@ -1,11 +1,11 @@
 #
-# = test/bio/tc_pathway.rb - Unit test for Bio::Pathway
+# = test/unit/bio/test_reference.rb - Unit test for Bio::Reference
 #
 # Copyright::  Copyright (C) 2006 
 #              Mitsuteru C. Nakao <n@bioruby.org>
 # License::    The Ruby License
 #
-# $Id: test_reference.rb,v 1.3.2.2 2008/06/17 12:24:41 ngoto Exp $
+# $Id:$
 #
 
 require 'pathname'
@@ -199,25 +199,25 @@ __END__
 
   end
 
-  class NullStderr
-    def initialize
-      @log = []
-    end
+  class TestReferences < Test::Unit::TestCase
 
-    def write(*arg)
-      #p arg
-      @log.push([ :write, *arg ])
-      nil
-    end
+    class NullStderr
+      def initialize
+        @log = []
+      end
 
-    def method_missing(*arg)
-      #p arg
-      @log.push arg
-      nil
-    end
-  end
+      def write(*arg)
+        #p arg
+        @log.push([ :write, *arg ])
+        nil
+      end
 
-  class TestReferences < Test::Unit::TestCase
+      def method_missing(*arg)
+        #p arg
+        @log.push arg
+        nil
+      end
+    end #class NullStderr
 
     def setup
       # To suppress warning messages, $stderr is replaced by dummy object.

data/test/unit/bio/test_sequence.rb

@@ -321,7 +321,7 @@ module Bio
     def test_translate_5
       assert_equal("", @obj.translate(5))
     end
-    def test_translate_5
+    def test_translate_6
       assert_equal("", @obj.translate(6))
     end
   end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification 
 name: bio
 version: !ruby/object:Gem::Version 
-  version: 1.3.0
+  version: 1.3.1
 platform: ruby
 authors: 
 - BioRuby project
@@ -9,7 +9,7 @@ autorequire: bio
 bindir: bin
 cert_chain: []
 
-date: 2009-02-20 00:00:00 +09:00
+date: 2009-09-02 00:00:00 +09:00
 default_executable: bioruby
 dependencies: []
 
@@ -30,8 +30,13 @@ extra_rdoc_files:
 - README_DEV.rdoc
 - doc/Changes-1.3.rdoc
 files: 
+- COPYING
+- COPYING.ja
 - ChangeLog
+- GPL
 - KNOWN_ISSUES.rdoc
+- LEGAL
+- LGPL
 - README.rdoc
 - README_DEV.rdoc
 - Rakefile
@@ -169,35 +174,9 @@ files:
 - lib/bio/db/soft.rb
 - lib/bio/db/transfac.rb
 - lib/bio/feature.rb
-- lib/bio/io/biosql/biodatabase.rb
-- lib/bio/io/biosql/bioentry.rb
-- lib/bio/io/biosql/bioentry_dbxref.rb
-- lib/bio/io/biosql/bioentry_path.rb
-- lib/bio/io/biosql/bioentry_qualifier_value.rb
-- lib/bio/io/biosql/bioentry_reference.rb
-- lib/bio/io/biosql/bioentry_relationship.rb
-- lib/bio/io/biosql/biosequence.rb
-- lib/bio/io/biosql/comment.rb
+- lib/bio/io/biosql/ar-biosql.rb
+- lib/bio/io/biosql/biosql.rb
 - lib/bio/io/biosql/config/database.yml
-- lib/bio/io/biosql/dbxref.rb
-- lib/bio/io/biosql/dbxref_qualifier_value.rb
-- lib/bio/io/biosql/location.rb
-- lib/bio/io/biosql/location_qualifier_value.rb
-- lib/bio/io/biosql/ontology.rb
-- lib/bio/io/biosql/reference.rb
-- lib/bio/io/biosql/seqfeature.rb
-- lib/bio/io/biosql/seqfeature_dbxref.rb
-- lib/bio/io/biosql/seqfeature_path.rb
-- lib/bio/io/biosql/seqfeature_qualifier_value.rb
-- lib/bio/io/biosql/seqfeature_relationship.rb
-- lib/bio/io/biosql/taxon.rb
-- lib/bio/io/biosql/taxon_name.rb
-- lib/bio/io/biosql/term.rb
-- lib/bio/io/biosql/term_dbxref.rb
-- lib/bio/io/biosql/term_path.rb
-- lib/bio/io/biosql/term_relationship.rb
-- lib/bio/io/biosql/term_relationship_term.rb
-- lib/bio/io/biosql/term_synonym.rb
 - lib/bio/io/das.rb
 - lib/bio/io/dbget.rb
 - lib/bio/io/ddbjxml.rb
@@ -361,6 +340,7 @@ files:
 - test/data/embl/AB090716.embl.rel89
 - test/data/fasta/example1.txt
 - test/data/fasta/example2.txt
+- test/data/gcg/pileup-aa.msf
 - test/data/genscan/sample.report
 - test/data/iprscan/merged.raw
 - test/data/iprscan/merged.txt
@@ -370,11 +350,15 @@ files:
 - test/data/prosite/prosite.dat
 - test/data/refseq/nm_126355.entret
 - test/data/rpsblast/misc.rpsblast
+- test/data/sim4/complement-A4.sim4
+- test/data/sim4/simple-A4.sim4
+- test/data/sim4/simple2-A4.sim4
 - test/data/soft/GDS100_partial.soft
 - test/data/soft/GSE3457_family_partial.soft
 - test/data/uniprot/p53_human.uniprot
 - test/functional/bio/appl/test_pts1.rb
 - test/functional/bio/io/test_ensembl.rb
+- test/functional/bio/io/test_pubmed.rb
 - test/functional/bio/io/test_soapwsdl.rb
 - test/functional/bio/io/test_togows.rb
 - test/functional/bio/sequence/test_output_embl.rb
@@ -384,6 +368,7 @@ files:
 - test/unit/bio/appl/blast/test_ncbioptions.rb
 - test/unit/bio/appl/blast/test_report.rb
 - test/unit/bio/appl/blast/test_rpsblast.rb
+- test/unit/bio/appl/gcg/test_msf.rb
 - test/unit/bio/appl/genscan/test_report.rb
 - test/unit/bio/appl/hmmer/test_report.rb
 - test/unit/bio/appl/iprscan/test_report.rb
@@ -391,6 +376,7 @@ files:
 - test/unit/bio/appl/paml/codeml/test_rates.rb
 - test/unit/bio/appl/paml/codeml/test_report.rb
 - test/unit/bio/appl/paml/test_codeml.rb
+- test/unit/bio/appl/sim4/test_report.rb
 - test/unit/bio/appl/sosui/test_report.rb
 - test/unit/bio/appl/targetp/test_report.rb
 - test/unit/bio/appl/test_blast.rb
@@ -400,6 +386,8 @@ files:
 - test/unit/bio/data/test_aa.rb
 - test/unit/bio/data/test_codontable.rb
 - test/unit/bio/data/test_na.rb
+- test/unit/bio/db/biosql/tc_biosql.rb
+- test/unit/bio/db/biosql/ts_suite_biosql.rb
 - test/unit/bio/db/embl/test_common.rb
 - test/unit/bio/db/embl/test_embl.rb
 - test/unit/bio/db/embl/test_embl_rel89.rb

data/lib/bio/io/biosql/biodatabase.rb

@@ -1,64 +0,0 @@
-module Bio
-		class SQL
-			class Biodatabase < DummyBase
-				has_many :bioentries, :class_name =>"Bioentry", :foreign_key => "biodatabase_id"
-				validates_uniqueness_of :name
-			end
-		end #SQL
-end #Bio	
-
-
-if __FILE__ == $0
-  require 'rubygems'
-  require 'composite_primary_keys'
-  require 'bio'
-  require 'pp'
-  
-  #  pp connection = Bio::SQL.establish_connection('bio/io/biosql/config/database.yml','development')
-  pp connection = Bio::SQL.establish_connection({'test'=>{'database'=>"bio_test", 'adapter'=>"postgresql", 'username'=>"rails", 'password'=>nil}},'test')
-  #pp YAML::load(ERB.new(IO.read('bio/io/biosql/config/database.yml')).result)
-  if true
-    pp Bio::SQL.list_entries
-
-    puts "### GenBank"
-    if ARGV.size > 0
-	gb = Bio::GenBank.new(ARGF.read)
-    else
-	require 'bio/io/fetch'
-	gb = Bio::GenBank.new(Bio::Fetch.query('gb', 'AJ224122'))
-    end
-
-   	biosequence = gb.to_biosequence
-	db=Bio::SQL::Biodatabase.new(:biodatabase_id=>3,:name=>"JEFF", :authority=>"ME", :description=>"YOU")
-	db.save!
-	
-	#sqlseq = Bio::SQL::Sequence.new(:biosequence=>biosequence,:biodatabase_id=>db.id)
-
-	#    bioseq = Bio::SQL.fetch_accession('AJ224122')   
-	#    pp bioseq
-	#    pp bioseq.entry_id    
-    #TODO create a test only for tables not sequence here
-#    pp bioseq.molecule_type
-    #pp  bioseq.molecule_type.class
-    #bioseq.molecule_type_update('dna', 1)
-    pp Bio::SQL::Taxon.find(8121).taxon_names
-    
-	    #sqlseq.to_biosequence
-	
-	#sqlseq.delete
-  end
-  #pp  bioseq.molecule_type
-  #term = Bio::SQL::Term.find_by_name('mol_type')
-  #pp term
-  #pp bioseq.entry.bioentry_qualifier_values.create(:term=>term, :rank=>2, :value=>'pippo')
-  #pp bioseq.entry.bioentry_qualifier_values.inspect
-  #pp bioseq.entry.bioentry_qualifier_values.find_all_by_term_id(26)
-  #pp primo.class
-  #  pp primo.value='dna'
-  #  pp primo.save
-  #pp bioseq.molecule_type= 'prova'
-  
-  #Bio::SQL::BioentryQualifierValue.delete(delete.bioentry_id,delete.term_id,delete.rank)
-  
-  
-end

data/lib/bio/io/biosql/bioentry.rb

@@ -1,29 +0,0 @@
-module Bio
-    class SQL
-			class Bioentry < DummyBase
-				belongs_to :biodatabase, :class_name => "Biodatabase"
-				belongs_to :taxon, :class_name => "Taxon"
-				has_one :biosequence
-				#, :class_name => "Biosequence", :foreign_key => "bioentry_id"
-				has_many :comments, :class_name =>"Comment", :order =>'rank'
-				has_many :seqfeatures, :class_name => "Seqfeature", :order=>'rank'
-				has_many :bioentry_references, :class_name=>"BioentryReference" #, :foreign_key => "bioentry_id"
-				has_many :bioentry_dbxrefs, :class_name => "BioentryDbxref"
-				has_many :object_bioentry_relationships, :class_name=>"BioentryRelationship", :foreign_key=>"object_bioentry_id" #non mi convince molto credo non funzioni nel modo corretto
-				has_many :subject_bioentry_relationships, :class_name=>"BioentryRelationship", :foreign_key=>"subject_bioentry_id" #non mi convince molto credo non funzioni nel modo corretto
-
-				has_many :cdsfeatures, :class_name=>"Seqfeature", :foreign_key =>"bioentry_id", :conditions=>["term.name='CDS'"], :include=>"type_term"
-        
-        has_many :terms, :through=>:bioentry_qualifier_values, :class_name => "Term"
-        #NOTE: added order_by for multiple hit and manage ranks correctly
-        has_many :bioentry_qualifier_values, :order=>"bioentry_id,term_id,rank", :class_name => "BioentryQualifierValue"
-        
-				#per la creazione richiesti:
-				#name, accession, version
-#				validates_uniqueness_of :accession, :scope=>[:biodatabase_id]
-#				validates_uniqueness_of :name, :scope=>[:biodatabase_id] 
-			#	validates_uniqueness_of :identifier, :scope=>[:biodatabase_id]
-				
-			end
-		end #SQL
-end #Bio