rbbt-sources 3.0.26 → 3.0.27

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: a288b1baadc35a9a6d906432ab6dfc79be6cdb85
+  metadata.gz: 181746bb32b62916dc308c6a3de563e9a4cabc38
+  data.tar.gz: 83716370f3b9b4b67001c027b2e92376d10e0470
 SHA512:
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+  data.tar.gz: 397844dfcd4b57939300c19e88de625291fb083dd1e380145f1edddfb30cbaca54c43d49bbb5981c92c8c47b257e0afc178204ba0e7ea34bba42777dec79b09d

data/lib/rbbt/sources/corum.rb

@@ -0,0 +1,45 @@
+require 'rbbt-util'
+require 'rbbt/resource'
+
+module CORUM
+  extend Resource
+  self.subdir = 'share/databases/CORUM'
+
+  def self.organism(org="Hsa")
+    Organism.default_code(org)
+  end
+
+  CORUM.claim CORUM.complex_names, :proc do 
+    url = "http://mips.helmholtz-muenchen.de/genre/proj/corum/allComplexes.csv"
+    tsv = TSV.open(url, :header_hash => "", :sep => ';', :sep2 => ',', :fix => Proc.new{|l| "CORUM:" + l.gsub('"','')})
+    tsv.namespace = organism
+    tsv.fields = tsv.fields.collect{|f| f.gsub('"','')}
+    tsv.key_field = "CORUM Complex ID"
+    tsv.slice("Complex name").to_single
+  end
+
+  CORUM.claim CORUM.complexes, :proc do 
+    url = "http://mips.helmholtz-muenchen.de/genre/proj/corum/allComplexes.csv"
+    tsv = TSV.open(url, :header_hash => "", :sep => ';', :sep2 => ',', :fix => Proc.new{|l| "CORUM:" + l.gsub('"','')})
+    tsv.namespace = organism
+    tsv.fields = tsv.fields.collect{|f| f.gsub('"','')}
+    tsv.key_field = "CORUM Complex ID"
+    tsv.identifiers = CORUM.complex_names.produce.find
+    tsv
+  end
+
+end
+
+if defined? Entity
+  module CORUMComplex
+    extend Entity
+
+    self.annotation :format
+    self.annotation :organism
+    self.add_identifiers CORUM.complex_names, "CORUM Complex ID", "Complex name"
+
+    property :genes => :array2single do
+      @genes ||= CORUM.complexes.tsv(:persist => true, :fields => ["subunits (UniProt IDs)"], :type => :flat).values_at *self
+    end
+  end
+end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-sources
 version: !ruby/object:Gem::Version
-  version: 3.0.26
+  version: 3.0.27
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-05-28 00:00:00.000000000 Z
+date: 2015-06-08 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util
@@ -99,6 +99,7 @@ files:
 - lib/rbbt/sources/bibtex.rb
 - lib/rbbt/sources/biomart.rb
 - lib/rbbt/sources/cath.rb
+- lib/rbbt/sources/corum.rb
 - lib/rbbt/sources/ensembl.rb
 - lib/rbbt/sources/ensembl_ftp.rb
 - lib/rbbt/sources/entrez.rb