bio-biosql 0.0.0
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- 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
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This is a dummy file to prevent removal of this directory.
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# To change this template, choose Tools | Templates
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# and open the template in the editor.
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# loading helper routine for testing bioruby
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require 'pathname'
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load Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4,
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'bioruby_test_helper.rb')).cleanpath.to_s
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# libraries needed for the tests
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require 'test/unit'
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require 'bio'
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module Bio
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class TestBiosqlIO < Test::Unit::TestCase
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def setup
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@connection = Bio::SQL.establish_connection({'development'=>{'hostname'=>'localhost','database'=>"bioseq", 'adapter'=>"jdbcmysql", 'username'=>"febo", 'password'=>nil}},'development')
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@str_genbank=<<END
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LOCUS X64011 756 bp DNA linear BCT 26-SEP-2006
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DEFINITION Listeria ivanovii sod gene for superoxide dismutase.
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ACCESSION X64011 S78972
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VERSION X64011.1 GI:44010
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KEYWORDS sod gene; superoxide dismutase.
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SOURCE Listeria ivanovii
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ORGANISM Listeria ivanovii
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Bacteria; Firmicutes; Bacillales; Listeriaceae; Listeria.
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REFERENCE 1
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AUTHORS Haas,A. and Goebel,W.
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TITLE Cloning of a superoxide dismutase gene from Listeria ivanovii by
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functional complementation in Escherichia coli and characterization
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of the gene product
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JOURNAL Mol. Gen. Genet. 231 (2), 313-322 (1992)
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PUBMED 1736100
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REFERENCE 2 (bases 1 to 756)
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AUTHORS Kreft,J.
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TITLE Direct Submission
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JOURNAL Submitted (21-APR-1992) J. Kreft, Institut f. Mikrobiologie,
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Universitaet Wuerzburg, Biozentrum Am Hubland, 8700 Wuerzburg, FRG
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COMMENT On Jun 23, 2005 this sequence version replaced gi:244394.
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FEATURES Location/Qualifiers
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source 1..756
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/organism="Listeria ivanovii"
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/mol_type="genomic DNA"
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/strain="ATCC 19119"
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/db_xref="taxon:1638"
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gene 95..746
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/gene="sod"
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RBS 95..100
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/gene="sod"
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CDS 109..717
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/gene="sod"
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/EC_number="1.15.1.1"
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/codon_start=1
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/transl_table=11
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/product="superoxide dismutase"
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/protein_id="CAA45406.1"
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/db_xref="GI:44011"
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/db_xref="GOA:P28763"
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/db_xref="InterPro:IPR001189"
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/db_xref="UniProtKB/Swiss-Prot:P28763"
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/translation="MTYELPKLPYTYDALEPNFDKETMEIHYTKHHNIYVTKLNEAVS
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GHAELASKPGEELVANLDSVPEEIRGAVRNHGGGHANHTLFWSSLSPNGGGAPTGNLK
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AAIESEFGTFDEFKEKFNAAAAARFGSGWAWLVVNNGKLEIVSTANQDSPLSEGKTPV
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LGLDVWEHAYYLKFQNRRPEYIDTFWNVINWDERNKRFDAAK"
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terminator 723..746
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/gene="sod"
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ORIGIN
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1 cgttatttaa ggtgttacat agttctatgg aaatagggtc tatacctttc gccttacaat
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61 gtaatttctt ttcacataaa taataaacaa tccgaggagg aatttttaat gacttacgaa
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121 ttaccaaaat taccttatac ttatgatgct ttggagccga attttgataa agaaacaatg
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181 gaaattcact atacaaagca ccacaatatt tatgtaacaa aactaaatga agcagtctca
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241 ggacacgcag aacttgcaag taaacctggg gaagaattag ttgctaatct agatagcgtt
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301 cctgaagaaa ttcgtggcgc agtacgtaac cacggtggtg gacatgctaa ccatacttta
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361 ttctggtcta gtcttagccc aaatggtggt ggtgctccaa ctggtaactt aaaagcagca
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421 atcgaaagcg aattcggcac atttgatgaa ttcaaagaaa aattcaatgc ggcagctgcg
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481 gctcgttttg gttcaggatg ggcatggcta gtagtgaaca atggtaaact agaaattgtt
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541 tccactgcta accaagattc tccacttagc gaaggtaaaa ctccagttct tggcttagat
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601 gtttgggaac atgcttatta tcttaaattc caaaaccgtc gtcctgaata cattgacaca
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661 ttttggaatg taattaactg ggatgaacga aataaacgct ttgacgcagc aaaataatta
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721 tcgaaaggct cacttaggtg ggtcttttta tttcta
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//
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END
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end
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def test_00_connection
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assert_instance_of(ActiveRecord::ConnectionAdapters::ConnectionPool, @connection)
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end
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def test_01_input_is_genbank
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assert_instance_of(Bio::GenBank,Bio::GenBank.new(@str_genbank))
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end
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def test_02_insert_bioentry
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@@x = Bio::SQL::Sequence.new(:biosequence=>Bio::GenBank.new(@str_genbank).to_biosequence, :biodatabase=>Bio::SQL::Biodatabase.find(:first))
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assert_not_nil(@@x)
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end
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def test_03_input_output
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bioseq = Bio::SQL.fetch_accession("X64011")
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assert_not_nil bioseq
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assert_equal(@str_genbank, bioseq.to_biosequence.output(:genbank))
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end
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def test_04_bioentry_data_format
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assert_equal('26-SEP-2006', @@x.date_modified.to_s)
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end
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def test_05_title
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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)
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end
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def test_99_delete_bioentry
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assert_not_nil(@@x.delete)
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end
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end
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end
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metadata
ADDED
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--- !ruby/object:Gem::Specification
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name: bio-biosql
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version: !ruby/object:Gem::Version
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version: 0.0.0
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platform: ruby
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authors:
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- BioRuby project
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2016-06-17 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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name: bio
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requirement: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: 1.5.0
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type: :runtime
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: 1.5.0
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- !ruby/object:Gem::Dependency
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name: activerecord
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requirement: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: 3.0.10
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type: :runtime
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: 3.0.10
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- !ruby/object:Gem::Dependency
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name: composite_primary_keys
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requirement: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: 3.1.10
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type: :runtime
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: 3.1.10
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- !ruby/object:Gem::Dependency
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name: bundler
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requirement: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '1.7'
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type: :development
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '1.7'
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- !ruby/object:Gem::Dependency
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name: rake
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requirement: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '10.0'
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type: :development
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '10.0'
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- !ruby/object:Gem::Dependency
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name: rdoc
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requirement: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '4'
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type: :development
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '4'
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- !ruby/object:Gem::Dependency
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name: test-unit
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requirement: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '3'
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type: :development
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prerelease: false
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version_requirements: !ruby/object:Gem::Requirement
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requirements:
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- - "~>"
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- !ruby/object:Gem::Version
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version: '3'
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description: Provides BioSQL support for BioRuby.
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email:
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- staff@bioruby.org
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executables: []
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extensions: []
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extra_rdoc_files:
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- README.md
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- COPYING
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- COPYING.ja
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- BSDL
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files:
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- ".gitignore"
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- ".project"
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- BSDL
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- COPYING
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126
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- COPYING.ja
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127
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- Gemfile
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128
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- LEGAL
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129
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- README.md
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- Rakefile
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131
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- bio-biosql.gemspec
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132
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- lib/bio-biosql/version.rb
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133
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- lib/bio/db/biosql/biosql_to_biosequence.rb
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134
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- lib/bio/db/biosql/sequence.rb
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135
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- lib/bio/io/biosql/ar-biosql.rb
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136
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- lib/bio/io/biosql/biosql.rb
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137
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- lib/bio/io/biosql/config/database.yml
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- lib/bio/io/sql.rb
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139
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- test/bioruby_test_helper.rb
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140
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- test/data/00dummy.txt
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141
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- test/unit/bio/db/biosql/tc_biosql.rb
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142
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- test/unit/bio/db/biosql/ts_suite_biosql.rb
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homepage: http://github.com/bioruby/bioruby-biosql
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licenses:
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- Ruby
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metadata: {}
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post_install_message:
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rdoc_options:
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- "--main"
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- README.md
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- "--title"
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- Bio::SQL API documentation
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- "--line-numbers"
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require_paths:
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- lib
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156
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required_ruby_version: !ruby/object:Gem::Requirement
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requirements:
|
158
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- - ">="
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159
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- !ruby/object:Gem::Version
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160
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version: '0'
|
161
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required_rubygems_version: !ruby/object:Gem::Requirement
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162
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requirements:
|
163
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- - ">="
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164
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- !ruby/object:Gem::Version
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version: '0'
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166
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requirements: []
|
167
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rubyforge_project:
|
168
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rubygems_version: 2.4.5.1
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signing_key:
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170
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specification_version: 4
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summary: BioSQL plugin for BioRuby
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172
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test_files:
|
173
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- test/bioruby_test_helper.rb
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174
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- test/data/00dummy.txt
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175
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- test/unit/bio/db/biosql/tc_biosql.rb
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176
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- test/unit/bio/db/biosql/ts_suite_biosql.rb
|