RubyGems - bio-biosql - Versions diffs - 0.0.0 - Mend

bio-biosql 0.0.0

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Files changed (23) hide show

checksums.yaml +7 -0
data/.gitignore +14 -0
data/.project +17 -0
data/BSDL +22 -0
data/COPYING +56 -0
data/COPYING.ja +51 -0
data/Gemfile +4 -0
data/LEGAL +9 -0
data/README.md +69 -0
data/Rakefile +19 -0
data/bio-biosql.gemspec +36 -0
data/lib/bio-biosql/version.rb +5 -0
data/lib/bio/db/biosql/biosql_to_biosequence.rb +78 -0
data/lib/bio/db/biosql/sequence.rb +444 -0
data/lib/bio/io/biosql/ar-biosql.rb +257 -0
data/lib/bio/io/biosql/biosql.rb +39 -0
data/lib/bio/io/biosql/config/database.yml +21 -0
data/lib/bio/io/sql.rb +79 -0
data/test/bioruby_test_helper.rb +86 -0
data/test/data/00dummy.txt +1 -0
data/test/unit/bio/db/biosql/tc_biosql.rb +114 -0
data/test/unit/bio/db/biosql/ts_suite_biosql.rb +8 -0
metadata +176 -0

data/test/data/00dummy.txt ADDED

	@@ -0,0 +1 @@
1	+ This is a dummy file to prevent removal of this directory.

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

@@ -0,0 +1,114 @@
+# To change this template, choose Tools | Templates
+# and open the template in the editor.
+# loading helper routine for testing bioruby
+require 'pathname'
+load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
+                            'bioruby_test_helper.rb')).cleanpath.to_s
+# libraries needed for the tests
+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 ADDED

@@ -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'

metadata ADDED

@@ -0,0 +1,176 @@
+--- !ruby/object:Gem::Specification
+name: bio-biosql
+version: !ruby/object:Gem::Version
+  version: 0.0.0
+platform: ruby
+authors:
+- BioRuby project
+autorequire:
+bindir: bin
+cert_chain: []
+date: 2016-06-17 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bio
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 1.5.0
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 1.5.0
+- !ruby/object:Gem::Dependency
+  name: activerecord
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 3.0.10
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 3.0.10
+- !ruby/object:Gem::Dependency
+  name: composite_primary_keys
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 3.1.10
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: 3.1.10
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.7'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.7'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '4'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '4'
+- !ruby/object:Gem::Dependency
+  name: test-unit
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3'
+description: Provides BioSQL support for BioRuby.
+email:
+- staff@bioruby.org
+executables: []
+extensions: []
+extra_rdoc_files:
+- README.md
+- COPYING
+- COPYING.ja
+- BSDL
+files:
+- ".gitignore"
+- ".project"
+- BSDL
+- COPYING
+- COPYING.ja
+- Gemfile
+- LEGAL
+- README.md
+- Rakefile
+- bio-biosql.gemspec
+- lib/bio-biosql/version.rb
+- lib/bio/db/biosql/biosql_to_biosequence.rb
+- lib/bio/db/biosql/sequence.rb
+- lib/bio/io/biosql/ar-biosql.rb
+- lib/bio/io/biosql/biosql.rb
+- lib/bio/io/biosql/config/database.yml
+- lib/bio/io/sql.rb
+- test/bioruby_test_helper.rb
+- test/data/00dummy.txt
+- test/unit/bio/db/biosql/tc_biosql.rb
+- test/unit/bio/db/biosql/ts_suite_biosql.rb
+homepage: http://github.com/bioruby/bioruby-biosql
+licenses:
+- Ruby
+metadata: {}
+post_install_message:
+rdoc_options:
+- "--main"
+- README.md
+- "--title"
+- Bio::SQL API documentation
+- "--line-numbers"
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project:
+rubygems_version: 2.4.5.1
+signing_key:
+specification_version: 4
+summary: BioSQL plugin for BioRuby
+test_files:
+- test/bioruby_test_helper.rb
+- test/data/00dummy.txt
+- test/unit/bio/db/biosql/tc_biosql.rb
+- test/unit/bio/db/biosql/ts_suite_biosql.rb