rbbt-sources 3.1.15 → 3.1.16

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 968b6c9ab9794fa92209ba2c8f36537bfc942711
-  data.tar.gz: 6a5501945048ef2a52872d54e35a85d8637b25a0
+  metadata.gz: feef731c1d37abc9fcaf618086634f4bebde968c
+  data.tar.gz: 58d28f8048a043d406c0cc1f72fe3b44186ead5e
 SHA512:
-  metadata.gz: 8ded417d4f6a04e6ff5ba21da1e454d54a0cf73aab95783a1a60ada25ea39faad2f8d4edcae462ae44f03de0ff488ea99737dc235d4472493d309342debe3391
-  data.tar.gz: 91b3fbe0852496b15cae6b512f150e5cf86c1742d57d41104b2247df3e75661dc5dce5aa4bae6e3eb86a3bd427addb842f97617a32a6f977a31fc0385daded3a
+  metadata.gz: b5fa5a78fe7e152691a92b6119202fdb0066fcf7377bafeb907b02519477221762c8b563239c26024700ee48f301e4377527f95441d87cadb50a26bc884dc626
+  data.tar.gz: cdb897373677da35b65aa93964af005ac1048a4097643a4ae0b1a67024f67dc90da5204b5eea928429039cc63c9da275c6faf3b99cc920f3e46ca893c8f3dcab

data/lib/rbbt/sources/oncodrive_role.rb

@@ -0,0 +1,32 @@
+require 'rbbt-util'
+require 'rbbt/resource'
+require 'rbbt/sources/organism'
+
+module OncoDriveROLE
+  extend Resource
+  self.subdir = 'share/databases/OncoDriveROLE'
+
+  def self.organism(org="Hsa")
+    Organism.default_code(org)
+  end
+
+  #self.search_paths = {}
+  #self.search_paths[:default] = :lib
+
+
+  OncoDriveROLE.claim OncoDriveROLE.Cancer5000, :proc do 
+    url = "http://bg.upf.edu/oncodrive-role/session/26f1ae8615a9420110c0b1b9f68d9c09/download/downloadData?w="
+    tsv = TSV.open(url, :header_hash => '', :type => :list, :namespace => OncoDriveROLE.organism)
+    tsv.key_field = "Ensembl Gene ID"
+    tsv.fields = ["Associated Gene Name", "Mode of action", "Value"]
+
+    tsv.to_s
+  end
+
+  def self.oncogenes
+    OncoDriveROLE.Cancer5000.tsv.select("Mode of action" => "Activating").keys
+  end
+end
+
+iif OncoDriveROLE.Cancer5000.produce.find if __FILE__ == $0
+

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-sources
 version: !ruby/object:Gem::Version
-  version: 3.1.15
+  version: 3.1.16
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-04-18 00:00:00.000000000 Z
+date: 2017-06-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util
@@ -111,6 +111,7 @@ files:
 - lib/rbbt/sources/jochem.rb
 - lib/rbbt/sources/kegg.rb
 - lib/rbbt/sources/matador.rb
+- lib/rbbt/sources/oncodrive_role.rb
 - lib/rbbt/sources/organism.rb
 - lib/rbbt/sources/pfam.rb
 - lib/rbbt/sources/pharmagkb.rb
@@ -181,19 +182,19 @@ signing_key:
 specification_version: 4
 summary: Data sources for the Ruby Bioinformatics Toolkit (rbbt)
 test_files:
+- test/test_helper.rb
 - test/rbbt/sources/test_pubmed.rb
-- test/rbbt/sources/test_pharmagkb.rb
-- test/rbbt/sources/test_biomart.rb
+- test/rbbt/sources/test_string.rb
 - test/rbbt/sources/test_gscholar.rb
-- test/rbbt/sources/test_kegg.rb
+- test/rbbt/sources/test_biomart.rb
+- test/rbbt/sources/test_go.rb
 - test/rbbt/sources/test_pina.rb
 - test/rbbt/sources/test_entrez.rb
+- test/rbbt/sources/test_pharmagkb.rb
+- test/rbbt/sources/test_organism.rb
 - test/rbbt/sources/test_matador.rb
-- test/rbbt/sources/test_HPRD.rb
+- test/rbbt/sources/test_tfacts.rb
+- test/rbbt/sources/test_kegg.rb
 - test/rbbt/sources/test_synapse.rb
-- test/rbbt/sources/test_go.rb
 - test/rbbt/sources/test_stitch.rb
-- test/rbbt/sources/test_organism.rb
-- test/rbbt/sources/test_string.rb
-- test/rbbt/sources/test_tfacts.rb
-- test/test_helper.rb
+- test/rbbt/sources/test_HPRD.rb