rbbt-sources 1.2.0 → 2.0.0

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File without changes
@@ -1,17 +1,22 @@
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  require File.expand_path(File.dirname(__FILE__) + '/../../test_helper')
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  require 'rbbt/sources/organism'
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  require 'test/unit'
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+ require 'rbbt/sources/ensembl_ftp'
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+
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+ class TestOrganism < Test::Unit::TestCase
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+
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+ def test_known_ids
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+ assert Organism.known_ids("Hsa").include?("Associated Gene Name")
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+ end
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- class TestEntrez < Test::Unit::TestCase
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  def test_location
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  assert_equal "share/organisms/Sce/identifiers", Organism.identifiers('Sce')
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  end
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-
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  def test_identifiers
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  assert Organism.identifiers('Hsa').tsv(:key_field => "Entrez Gene ID", :persist => true)['1020']["Associated Gene Name"].include?('CDK5')
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  assert Organism.identifiers('Sce').tsv(:persist => true)['S000006120']["Ensembl Gene ID"].include?('YPL199C')
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- assert Organism::Sce.identifiers.tsv(:persist => true)['S000006120']["Ensembl Gene ID"].include?('YPL199C')
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+ assert Organism.identifiers("Sce").tsv(:persist => true)['S000006120']["Ensembl Gene ID"].include?('YPL199C')
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  end
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  def test_lexicon
@@ -21,8 +26,8 @@ class TestEntrez < Test::Unit::TestCase
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  def test_guess_id
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  ensembl = %w(YOL044W YDR289C YAL034C YGR246C ARS519 tH(GUG)E2 YDR218C YLR002C YGL224C)
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  gene_name = %w(SNR64 MIP1 MRPS18 TFB2 JEN1 IVY1 TRS33 GAS3)
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- assert_equal "Associated Gene Name", Organism::Sce.guess_id(gene_name).first
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- assert_equal "Ensembl Gene ID", Organism::Sce.guess_id(ensembl).first
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+ assert_equal "Associated Gene Name", Organism.guess_id("Sce", gene_name).first
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+ assert_equal "Ensembl Gene ID", Organism.guess_id("Sce", ensembl).first
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  end
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  def test_organisms
@@ -36,12 +41,26 @@ class TestEntrez < Test::Unit::TestCase
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  tsv.fields = []
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  tsv.namespace = "Hsa"
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- Organism::Hsa.attach_translations tsv, "Associated Gene Name"
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- Organism::Hsa.attach_translations tsv, "Ensembl Gene ID"
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+ Organism.attach_translations "Hsa", tsv, "Associated Gene Name"
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+ Organism.attach_translations "Hsa", tsv, "Ensembl Gene ID"
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  assert_equal "CDK5", tsv["1020"]["Associated Gene Name"]
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  end
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+ def test_entrez_taxids
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+ assert_equal "Hsa", Organism.entrez_taxid_organism('9606')
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+ end
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+
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+ def test_lift_over
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+ mutation_19 = "19:21131664:T"
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+ mutation_18 = "19:20923504:T"
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+ source_build = "Hsa/jun2011"
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+ target_build = "Hsa/may2009"
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+
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+ assert_equal mutation_18, Organism.liftOver([mutation_19], source_build, target_build).first
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+ assert_equal mutation_19, Organism.liftOver([mutation_18], target_build, source_build).first
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+ end
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+
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  #def test_genes_at_chromosome
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  # pos = [12, 117799500]
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  # assert_equal "ENSG00000089250", Organism::Hsa.genes_at_chromosome_positions(pos.first, pos.last)
@@ -30,6 +30,11 @@ class TestPubMed < Test::Unit::TestCase
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  assert(PubMed.query('chagoyen[All Fields] AND ("loattrfull text"[sb] AND hasabstract[text])').include? '16438716')
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  end
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+ def test_year
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+ pmid = '16438716'
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+ assert_equal "2006", PubMed.get_article(pmid).year
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+ end
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+
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  def test_bibentry
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  assert("vazquez2008sent", PubMed::Article.make_bibentry('vazquez', 2008, "SENT: Semantic features in text"))
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  assert("vazquez2008aes", PubMed::Article.make_bibentry('vazquez', 2008, "An Example System"))
metadata CHANGED
@@ -1,115 +1,119 @@
1
- --- !ruby/object:Gem::Specification
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+ --- !ruby/object:Gem::Specification
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  name: rbbt-sources
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- version: !ruby/object:Gem::Version
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- hash: 31
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+ version: !ruby/object:Gem::Version
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+ version: 2.0.0
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  prerelease:
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- segments:
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- - 1
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- - 2
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- - 0
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- version: 1.2.0
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  platform: ruby
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- authors:
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+ authors:
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  - Miguel Vazquez
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  autorequire:
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  bindir: bin
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  cert_chain: []
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-
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- date: 2012-01-13 00:00:00 +01:00
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- default_executable:
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- dependencies:
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- - !ruby/object:Gem::Dependency
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+ date: 2012-12-21 00:00:00.000000000 Z
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+ dependencies:
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+ - !ruby/object:Gem::Dependency
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  name: rbbt-util
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- prerelease: false
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- requirement: &id001 !ruby/object:Gem::Requirement
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+ requirement: !ruby/object:Gem::Requirement
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  none: false
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- requirements:
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- - - ">="
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- - !ruby/object:Gem::Version
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- hash: 63
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- segments:
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- - 4
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- - 0
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- - 0
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+ requirements:
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+ - - ! '>='
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+ - !ruby/object:Gem::Version
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  version: 4.0.0
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  type: :runtime
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- version_requirements: *id001
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- - !ruby/object:Gem::Dependency
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- name: rbbt-text
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  prerelease: false
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- requirement: &id002 !ruby/object:Gem::Requirement
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+ version_requirements: !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ! '>='
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+ - !ruby/object:Gem::Version
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+ version: 4.0.0
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+ - !ruby/object:Gem::Dependency
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+ name: rbbt-text
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+ requirement: !ruby/object:Gem::Requirement
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  none: false
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- requirements:
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- - - ">="
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- - !ruby/object:Gem::Version
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- hash: 3
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- segments:
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- - 0
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- version: "0"
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+ requirements:
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+ - - ! '>='
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+ - !ruby/object:Gem::Version
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+ version: '0'
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  type: :runtime
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- version_requirements: *id002
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- - !ruby/object:Gem::Dependency
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- name: mechanize
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  prerelease: false
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- requirement: &id003 !ruby/object:Gem::Requirement
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+ version_requirements: !ruby/object:Gem::Requirement
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  none: false
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- requirements:
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- - - ">="
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- - !ruby/object:Gem::Version
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- hash: 3
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- segments:
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- - 0
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- version: "0"
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- type: :runtime
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- version_requirements: *id003
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- - !ruby/object:Gem::Dependency
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+ requirements:
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+ - - ! '>='
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ - !ruby/object:Gem::Dependency
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  name: libxml-ruby
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- prerelease: false
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- requirement: &id004 !ruby/object:Gem::Requirement
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+ requirement: !ruby/object:Gem::Requirement
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  none: false
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- requirements:
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- - - ">="
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- - !ruby/object:Gem::Version
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- hash: 3
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- segments:
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- - 0
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- version: "0"
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+ requirements:
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+ - - ! '>='
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+ - !ruby/object:Gem::Version
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+ version: '0'
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  type: :runtime
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- version_requirements: *id004
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- - !ruby/object:Gem::Dependency
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ! '>='
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+ - !ruby/object:Gem::Version
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+ version: '0'
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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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+ none: false
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+ requirements:
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+ - - ! '>='
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ type: :runtime
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  prerelease: false
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- requirement: &id005 !ruby/object:Gem::Requirement
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+ version_requirements: !ruby/object:Gem::Requirement
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  none: false
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- requirements:
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- - - ">="
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- - !ruby/object:Gem::Version
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- hash: 3
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- segments:
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- - 0
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- version: "0"
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+ requirements:
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+ - - ! '>='
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ - !ruby/object:Gem::Dependency
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+ name: mechanize
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+ requirement: !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ! '>='
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+ - !ruby/object:Gem::Version
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+ version: '0'
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  type: :runtime
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- version_requirements: *id005
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ! '>='
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+ - !ruby/object:Gem::Version
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+ version: '0'
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  description: Data sources like PubMed, Entrez Gene, or Gene Ontology
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  email: miguel.vazquez@fdi.ucm.es
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  executables: []
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-
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  extensions: []
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-
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  extra_rdoc_files: []
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-
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- files:
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+ files:
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  - etc/biomart/missing_in_archive
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  - lib/rbbt/sources/COSMIC.rb
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  - lib/rbbt/sources/COSTART.rb
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  - lib/rbbt/sources/CTCAE.rb
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+ - lib/rbbt/sources/HPRD.rb
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  - lib/rbbt/sources/InterPro.rb
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  - lib/rbbt/sources/NCI.rb
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+ - lib/rbbt/sources/PSI_MI.rb
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+ - lib/rbbt/sources/STITCH.rb
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  - lib/rbbt/sources/barcode.rb
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  - lib/rbbt/sources/bibtex.rb
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  - lib/rbbt/sources/biomart.rb
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  - lib/rbbt/sources/cath.rb
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+ - lib/rbbt/sources/dbSNP.rb
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+ - lib/rbbt/sources/ensembl_ftp.rb
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  - lib/rbbt/sources/entrez.rb
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+ - lib/rbbt/sources/genomes1000.rb
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  - lib/rbbt/sources/go.rb
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  - lib/rbbt/sources/gscholar.rb
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  - lib/rbbt/sources/jochem.rb
@@ -117,10 +121,12 @@ files:
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  - lib/rbbt/sources/pfam.rb
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  - lib/rbbt/sources/polysearch.rb
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  - lib/rbbt/sources/pubmed.rb
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+ - lib/rbbt/sources/reactome.rb
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  - lib/rbbt/sources/tfacts.rb
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  - lib/rbbt/sources/uniprot.rb
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  - lib/rbbt/sources/wgEncodeBroadHmm.rb
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- - share/install/InterPro/Rakefile
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+ - share/Ensembl/release_dates
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+ - share/install/Genomes1000/Rakefile
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  - share/install/JoChem/Rakefile
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  - share/install/NCI/Rakefile
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  - share/install/Organism/Hsa/Rakefile
@@ -128,6 +134,7 @@ files:
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  - share/install/Organism/Rno/Rakefile
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  - share/install/Organism/Sce/Rakefile
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  - share/install/Organism/organism_helpers.rb
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+ - share/install/STITCH/Rakefile
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  - share/install/lib/helpers.rb
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  - test/test_helper.rb
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  - test/rbbt/sources/test_entrez.rb
@@ -135,41 +142,31 @@ files:
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  - test/rbbt/sources/test_go.rb
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  - test/rbbt/sources/test_biomart.rb
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  - test/rbbt/sources/test_organism.rb
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- has_rdoc: true
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  homepage: http://github.com/mikisvaz/rbbt-sources
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  licenses: []
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-
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  post_install_message:
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  rdoc_options: []
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-
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- require_paths:
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+ require_paths:
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  - lib
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- required_ruby_version: !ruby/object:Gem::Requirement
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+ required_ruby_version: !ruby/object:Gem::Requirement
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  none: false
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- requirements:
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- - - ">="
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- - !ruby/object:Gem::Version
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- hash: 3
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- segments:
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- - 0
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- version: "0"
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- required_rubygems_version: !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: '0'
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+ required_rubygems_version: !ruby/object:Gem::Requirement
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  none: false
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- requirements:
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- - - ">="
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- - !ruby/object:Gem::Version
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- hash: 3
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- segments:
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- - 0
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- version: "0"
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+ requirements:
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+ - - ! '>='
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+ - !ruby/object:Gem::Version
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+ version: '0'
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  requirements: []
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-
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164
  rubyforge_project:
168
- rubygems_version: 1.6.2
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+ rubygems_version: 1.8.24
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  signing_key:
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  specification_version: 3
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168
  summary: Data sources for the Ruby Bioinformatics Toolkit (rbbt)
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- test_files:
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+ test_files:
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  - test/test_helper.rb
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  - test/rbbt/sources/test_entrez.rb
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  - test/rbbt/sources/test_pubmed.rb
@@ -1,29 +0,0 @@
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- $LOAD_PATH.unshift(File.join(File.dirname(__FILE__),'..', '..', '..', '..', 'lib'))
2
- require 'rbbt/sources/biomart'
3
- require 'rbbt/sources/entrez'
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-
5
- $interpro_db = 'entry'
6
-
7
- $interpro_id = ['InterPro Entry Accession','entry_id']
8
-
9
- $interpro_pos = [
10
- ["UniProt/SwissProt Accession", "protein_ac"],
11
- ["Match Start Position", "pos_from"],
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- ["Match Stop Position ", "pos_to"]
13
- ]
14
-
15
- file 'interpro_positions' do |t|
16
- Open.write(t.name, InterPro.tsv($interpro_db, $interpro_id, $interpro_pos, [], nil, :type => :double, :nocache => true).to_s)
17
- end
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-
19
- file 'interpro_names' do |t|
20
- Open.write(t.name, "#: :type=:list\n#InterPro Entry Accession\tName\n" + Open.read("ftp://ftp.ebi.ac.uk/pub/databases/interpro/names.dat"))
21
- end
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-
23
-
24
- file 'interpro_short_names' do |t|
25
- Open.write(t.name, "#: :type=:list\n#InterPro Entry Accession\tShort Name\n" + Open.read("ftp://ftp.ebi.ac.uk/pub/databases/interpro/short_names.dat"))
26
- end
27
-
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-
29
-