rbbt-sources 3.1.10 → 3.1.11

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 47f883226de2b2dd6a0d9a91473aa012d2930f21
-  data.tar.gz: db8145fdcc9052ee7db1d7934153c623b0ab77b5
+  metadata.gz: 9883483307ee8d88dcc1b7a8ce6e82e2a1521f7e
+  data.tar.gz: ce5f86b1db3b370ccb53539641de478fb5aef1e3
 SHA512:
-  metadata.gz: d28848abcab0fd26b016f1e50a53572d338d8cd8de02d451730f49199ba39e5453033b286297aeaaa29e71f3a30dd7eebb92c43cf3fae5344298f3a7ce202099
-  data.tar.gz: 8e6763e6d1a082a907735444dd81424a18179ab68b65e2705708b6d5d440a6ec8a1a5658d51310a5558562e7cdf9f42cc8d6d14e3e81a6365a4b2fc339331a9a
+  metadata.gz: 312842cd07dc73920d0e346d43d4c228c0d48c4d441b421fb5b27e975d7a42fe72af1ccfa864695e86d4b63c1621f4b3731f39ae7f17e105b3ea544eb198fd27
+  data.tar.gz: d0c9288317e0cdf83a2862c79e0c8713bf521c1c1e0596d7e6c91ba01a38cdc6b2d953f9ff8b8674fd63a34807876e390927fc525e1102cbe57e87d80486f076

data/lib/rbbt/sources/tfacts.rb

@@ -27,15 +27,17 @@ module TFacts
   TFacts.claim TFacts.targets_signed, :proc do
     require 'spreadsheet'
     book = Spreadsheet.open TFacts[".source"]["Catalogues.xls"].produce.find
-    sheet = book.worksheet 0
+    sheet = book.worksheet 1
 
-    tsv = TSV.setup({}, :key_field => "Target Gene (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", "PMID"], :namespace => "Hsa", :type => :double)
     sheet.each do |row|
-      target, tf, sign = row.values_at 0, 1, 2
+      target, tf, sign, pmid = row.values_at(0, 1, 2, 5).collect{|e| e.to_s.gsub("\n", " ") }
+      pmid = pmid.split(";").select{|p| p =~ /^\d{5,}$/ }
       next if tf =~ /OFFICIAL_/
-      tsv[target] ||= [[],[]]
+      tsv[target] ||= [[],[],[]]
       tsv[target][0] << tf
       tsv[target][1] << sign
+      tsv[target][2] << pmid * ";"
     end
 
     tsv.to_s

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-sources
 version: !ruby/object:Gem::Version
-  version: 3.1.10
+  version: 3.1.11
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-02-15 00:00:00.000000000 Z
+date: 2017-02-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util
@@ -180,19 +180,19 @@ 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_string.rb
-- test/rbbt/sources/test_gscholar.rb
+- test/rbbt/sources/test_pharmagkb.rb
 - test/rbbt/sources/test_biomart.rb
-- test/rbbt/sources/test_go.rb
+- test/rbbt/sources/test_gscholar.rb
+- test/rbbt/sources/test_kegg.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_tfacts.rb
-- test/rbbt/sources/test_kegg.rb
+- test/rbbt/sources/test_HPRD.rb
 - test/rbbt/sources/test_synapse.rb
+- test/rbbt/sources/test_go.rb
 - test/rbbt/sources/test_stitch.rb
-- test/rbbt/sources/test_HPRD.rb
+- test/rbbt/sources/test_organism.rb
+- test/rbbt/sources/test_string.rb
+- test/rbbt/sources/test_tfacts.rb
+- test/test_helper.rb