rbbt-sources 3.1.18 → 3.1.19

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: d6a24c95d852df442ed303fe4fdc57b47b2fd0f2
-  data.tar.gz: ea6a37e44a97d4a8659a8d07ee58f7264fa50062
+  metadata.gz: 2e37f4f4156576088ee39f1836f07941e4a26619
+  data.tar.gz: 6f223756910829b3fc37348c93b7d7b73caa3e9f
 SHA512:
-  metadata.gz: a78985096754ac5d3689f06306c470b2f82334c9e427cb5efe05a88d78051fab07644e656f646079903eb2811642274039b6b71b8c233ef9e2f7fa45dd672add
-  data.tar.gz: 99004a5e7c6bc624f371f70306600cca13f915a13c2021c7ac50705206b6cc8df678d757843ab6e969c0b5dd4b453ce3e8f58d9ad0b9b766162e9042cb108842
+  metadata.gz: 8daf49212a7f547fb6c098b578c698daa5999b5d299b1f0435bb6b4437070ec8105488a4180c6b7726ab0f16498b32476bfdcc0e0af95e6ae910967aa6e044a0
+  data.tar.gz: 4661d5dd8c2d02ef2426d21fe42569b5eb536666929c1a66b0a171baf7f6db6756366b7683d4eec2eb1ec966410cd7f602e9ef8bd7a6a39ae55fdbf087dd31e2

data/lib/rbbt/sources/GTRD.rb

@@ -0,0 +1,23 @@
+require 'rbbt-util'
+require 'rbbt/resource'
+
+module GTRD
+  extend Resource
+  self.subdir = 'share/databases/GTRD'
+
+  def self.organism(org="Hsa")
+    Organism.default_code(org)
+  end
+
+  #self.search_paths = {}
+  #self.search_paths[:default] = :lib
+
+
+  GTRD.claim GTRD.tfClass, :proc do 
+    url = "http://gtrd.biouml.org/downloads/current/tfClass2ensembl.txt.gz"
+    CMD.cmd("grep Homo | cut -f 2", :in => Open.read(url)).read
+  end
+end
+
+iif GTRD.tfClass.produce.find if __FILE__ == $0
+

data/lib/rbbt/sources/corum.rb

@@ -11,7 +11,7 @@ module CORUM
   end
 
   CORUM.claim CORUM.complex_names, :proc do 
-    url = "http://mips.helmholtz-muenchen.de/corum/download/allComplexes.txt"
+    url = "http://mips.helmholtz-muenchen.de/corum/download/allComplexes.txt.zip"
     tsv = TSV.open(url, :header_hash => "", :sep2 => ';', :fix => Proc.new{|l| "CORUM:" + l.gsub('"','')})
     tsv.namespace = organism
     tsv.fields = tsv.fields.collect{|f| f.gsub('"','')}
@@ -22,7 +22,7 @@ module CORUM
   end
 
   CORUM.claim CORUM.complexes, :proc do 
-    url = "http://mips.helmholtz-muenchen.de/corum/download/allComplexes.txt"
+    url = "http://mips.helmholtz-muenchen.de/corum/download/allComplexes.txt.zip"
     tsv = TSV.open(url, :header_hash => "", :sep2 => ';', :fix => Proc.new{|l| "CORUM:" + l.gsub('"','')})
     tsv.namespace = organism
     tsv.fields = tsv.fields.collect{|f| f.gsub('"','')}.collect{|f|

data/lib/rbbt/sources/kegg.rb

@@ -3,8 +3,7 @@ require 'rbbt/resource'
 
 module KEGG
   extend Resource
-  self.pkgdir = "phgx"
-  self.subdir = "share/kegg"
+  self.subdir = "share/databases/kegg"
 
 
   KEGG.claim KEGG.root, :rake, Rbbt.share.install.KEGG.Rakefile.find(:lib)

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-sources
 version: !ruby/object:Gem::Version
-  version: 3.1.18
+  version: 3.1.19
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-08-14 00:00:00.000000000 Z
+date: 2017-09-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util
@@ -92,6 +92,7 @@ files:
 - lib/rbbt/sources/CASCADE.rb
 - lib/rbbt/sources/COSTART.rb
 - lib/rbbt/sources/CTCAE.rb
+- lib/rbbt/sources/GTRD.rb
 - lib/rbbt/sources/HPRD.rb
 - lib/rbbt/sources/MCLP.rb
 - lib/rbbt/sources/MSigDB.rb
@@ -181,7 +182,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.6.12
+rubygems_version: 2.6.13
 signing_key: 
 specification_version: 4
 summary: Data sources for the Ruby Bioinformatics Toolkit (rbbt)