rbbt-sources 3.1.9 → 3.1.10

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 4de6a2e2ce1b66916e6bfc8f0e336eca6b55e6a6
-  data.tar.gz: 5cae8b56631ed29ef195f22fc36c73015dce86eb
+  metadata.gz: 47f883226de2b2dd6a0d9a91473aa012d2930f21
+  data.tar.gz: db8145fdcc9052ee7db1d7934153c623b0ab77b5
 SHA512:
-  metadata.gz: c99d530f44054a5e2ddbb8dde13f182c1581172f73455051115045debb1efb140be2d42cb3c40e6156bfaf44bb3dc91c59d05af64967485031d9b81360a5e412
-  data.tar.gz: e4a3100bb65cbb65ca6ca7dec42c5f666b500157891a130cf34d86310aa544feac3739aae05efc347c47abf2195d05cf9d801dc218efe758066517f33e06ffec
+  metadata.gz: d28848abcab0fd26b016f1e50a53572d338d8cd8de02d451730f49199ba39e5453033b286297aeaaa29e71f3a30dd7eebb92c43cf3fae5344298f3a7ce202099
+  data.tar.gz: 8e6763e6d1a082a907735444dd81424a18179ab68b65e2705708b6d5d440a6ec8a1a5658d51310a5558562e7cdf9f42cc8d6d14e3e81a6365a4b2fc339331a9a

data/lib/rbbt/sources/tfacts.rb

@@ -4,18 +4,19 @@ require 'rbbt/resource'
 
 module TFacts
   extend Resource
-  self.subdir = "share/databases/TF"
+  self.subdir = "share/databases/TFacts"
 
-  TFacts.claim TFacts.source["Catalogues.xls"], :url, "http://www.tfacts.org/TFactS-new/TFactS-v2/tfacts/data/Catalogues.xls"
+  TFacts.claim TFacts[".source"]["Catalogues.xls"], :url, "http://www.tfacts.org/TFactS-new/TFactS-v2/tfacts/data/Catalogues.xls"
 
   TFacts.claim TFacts.targets, :proc do
     require 'spreadsheet'
-    book = Spreadsheet.open TFacts.source["Catalogues.xls"].produce.find
+    book = Spreadsheet.open TFacts[".source"]["Catalogues.xls"].produce.find
     sheet = book.worksheet 0
 
-    tsv = TSV.setup({}, :key_field => "Associated Gene Name", :fields => ["Transcription Factor Associated Gene Name"], :namespace => "Hsa", :type => :flat)
+    tsv = TSV.setup({}, :key_field => "Target Gene (Associated Gene Name)", :fields => ["Transcription Factor (Associated Gene Name)"], :namespace => "Hsa", :type => :flat)
     sheet.each do |row|
       target, tf = row.values_at 0, 1
+      next if tf =~ /OFFICIAL_/
       tsv[target] ||= []
       tsv[target] << tf
     end
@@ -25,12 +26,13 @@ module TFacts
 
   TFacts.claim TFacts.targets_signed, :proc do
     require 'spreadsheet'
-    book = Spreadsheet.open TFacts.source["Catalogues.xls"].produce.find
+    book = Spreadsheet.open TFacts[".source"]["Catalogues.xls"].produce.find
     sheet = book.worksheet 0
 
-    tsv = TSV.setup({}, :key_field => "Associated Gene Name", :fields => ["Transcription Factor Associated Gene Name", "Sign"], :namespace => "Hsa", :type => :double)
+    tsv = TSV.setup({}, :key_field => "Target Gene (Associated Gene Name)", :fields => ["Transcription Factor (Associated Gene Name)", "Sign"], :namespace => "Hsa", :type => :double)
     sheet.each do |row|
       target, tf, sign = row.values_at 0, 1, 2
+      next if tf =~ /OFFICIAL_/
       tsv[target] ||= [[],[]]
       tsv[target][0] << tf
       tsv[target][1] << sign
@@ -40,7 +42,7 @@ module TFacts
   end
 
   TFacts.claim TFacts.regulators, :proc do
-    TFacts.targets.tsv.reorder("Transcription Factor Associated Gene Name").to_s
+    TFacts.targets.tsv.reorder("Transcription Factor (Associated Gene Name)").to_s
   end
 
 end

data/share/install/Organism/organism_helpers.rb

@@ -414,6 +414,7 @@ file 'gene_go_bp' => 'gene_go' do |t|
   end
 
 
+  gene_go.filename = t.name
   Misc.sensiblewrite(t.name, gene_go.slice("GO ID").to_s)
 end
 
@@ -429,6 +430,7 @@ file 'gene_go_cc' => 'gene_go' do |t|
   end
 
 
+  gene_go.filename = t.name
   Misc.sensiblewrite(t.name, gene_go.slice("GO ID").to_s)
 end
 
@@ -444,6 +446,7 @@ file 'gene_go_mf' => 'gene_go' do |t|
   end
 
 
+  gene_go.filename = t.name
   Misc.sensiblewrite(t.name, gene_go.slice("GO ID").to_s)
 end
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-sources
 version: !ruby/object:Gem::Version
-  version: 3.1.9
+  version: 3.1.10
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-01-30 00:00:00.000000000 Z
+date: 2017-02-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util