rbbt-sources 3.1.15 → 3.1.16

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@@ -0,0 +1,32 @@
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+ require 'rbbt-util'
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+ require 'rbbt/resource'
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+ require 'rbbt/sources/organism'
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+
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+ module OncoDriveROLE
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+ extend Resource
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+ self.subdir = 'share/databases/OncoDriveROLE'
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+
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+ def self.organism(org="Hsa")
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+ Organism.default_code(org)
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+ end
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+
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+ #self.search_paths = {}
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+ #self.search_paths[:default] = :lib
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+
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+
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+ OncoDriveROLE.claim OncoDriveROLE.Cancer5000, :proc do
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+ url = "http://bg.upf.edu/oncodrive-role/session/26f1ae8615a9420110c0b1b9f68d9c09/download/downloadData?w="
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+ tsv = TSV.open(url, :header_hash => '', :type => :list, :namespace => OncoDriveROLE.organism)
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+ tsv.key_field = "Ensembl Gene ID"
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+ tsv.fields = ["Associated Gene Name", "Mode of action", "Value"]
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+
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+ tsv.to_s
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+ end
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+
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+ def self.oncogenes
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+ OncoDriveROLE.Cancer5000.tsv.select("Mode of action" => "Activating").keys
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+ end
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+ end
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+
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+ iif OncoDriveROLE.Cancer5000.produce.find if __FILE__ == $0
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+
metadata CHANGED
@@ -1,14 +1,14 @@
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1
  --- !ruby/object:Gem::Specification
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  name: rbbt-sources
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  version: !ruby/object:Gem::Version
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- version: 3.1.15
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+ version: 3.1.16
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  platform: ruby
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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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- date: 2017-04-18 00:00:00.000000000 Z
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+ date: 2017-06-15 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
@@ -111,6 +111,7 @@ files:
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  - lib/rbbt/sources/jochem.rb
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  - lib/rbbt/sources/kegg.rb
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  - lib/rbbt/sources/matador.rb
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+ - lib/rbbt/sources/oncodrive_role.rb
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  - lib/rbbt/sources/organism.rb
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  - lib/rbbt/sources/pfam.rb
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  - lib/rbbt/sources/pharmagkb.rb
@@ -181,19 +182,19 @@ signing_key:
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  specification_version: 4
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  summary: Data sources for the Ruby Bioinformatics Toolkit (rbbt)
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  test_files:
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+ - test/test_helper.rb
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  - test/rbbt/sources/test_pubmed.rb
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- - test/rbbt/sources/test_pharmagkb.rb
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- - test/rbbt/sources/test_biomart.rb
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+ - test/rbbt/sources/test_string.rb
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  - test/rbbt/sources/test_gscholar.rb
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- - test/rbbt/sources/test_kegg.rb
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+ - test/rbbt/sources/test_biomart.rb
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+ - test/rbbt/sources/test_go.rb
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  - test/rbbt/sources/test_pina.rb
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  - test/rbbt/sources/test_entrez.rb
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+ - test/rbbt/sources/test_pharmagkb.rb
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+ - test/rbbt/sources/test_organism.rb
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  - test/rbbt/sources/test_matador.rb
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- - test/rbbt/sources/test_HPRD.rb
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+ - test/rbbt/sources/test_tfacts.rb
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+ - test/rbbt/sources/test_kegg.rb
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  - test/rbbt/sources/test_synapse.rb
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- - test/rbbt/sources/test_go.rb
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  - test/rbbt/sources/test_stitch.rb
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- - test/rbbt/sources/test_organism.rb
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- - test/rbbt/sources/test_string.rb
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- - test/rbbt/sources/test_tfacts.rb
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- - test/test_helper.rb
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+ - test/rbbt/sources/test_HPRD.rb