rbbt-sources 3.2.1 → 3.2.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 973d827d476c42023692f813a588ad500da04dd27f6903e1da9c74673985b40e
-  data.tar.gz: ed995de19a62f17908c2b7ed3f327782c75ece60aa0f7c5f373cc9309228c8b5
+  metadata.gz: 45945055f3bb3f73e9928b667cfa01802910d9e5ae4d9cfb3df525d9958af872
+  data.tar.gz: '092951fa32efdc9ccabea467ccae1f4d7729cb0b7fa24b7c064b5a8671de66d8'
 SHA512:
-  metadata.gz: cff68ce8c57381ec1581a6df61b56d40384b108030f87858ea1a735a82b8922b9d71a8b8a42930846f30186610058cbf738dccfb788ebf49e3f4d5e1b000809f
-  data.tar.gz: 771625cad70732c54cc2a1b798f6c0ac44004e73a9435e6699a7988a0904e987fecd9e375e6f888061b0f88a4c03ff3200322c59ca75a7f8f83dcdad8b19b156
+  metadata.gz: 174dc33879a4c712a44a0574a9c772dcd06df4602f08d5ec4da98446c04297fd54104815ca5501c511d7599bf346a104bafe5744b6000b5c006117f6d21860d3
+  data.tar.gz: 4ff9086a6d2a83ad09823fd339bca8f4278958658faa20081f9f17f5ca7c500d569e76bf8bfd182ad742a9c8d823cd19a55d3eccd48c1e696046bfea32302366

data/lib/rbbt/sources/signor.rb

@@ -19,17 +19,7 @@ module Signor
   end
   
   Signor.claim Signor.data, :proc do
-    sio = Signor[".source/all.csv"].open
-    io_tmp = Misc.remove_quoted_new_line(sio)
-    io = Misc.swap_quoted_character(io_tmp, ';', '--SEMICOLON--')
-    
-    tsv = TSV.open io, :header_hash => "", :sep => ";", :merge => true, :type => :double, :zipped => true, :monitor => true
-    tsv.each do |k,values|
-      clean_values = values.collect{|vs| vs.collect{|v| (v[0] == '"' and v[-1] = '"') ? v[1..-2] : v }.collect{|v| v.gsub("--SEMICOLON--", ';') } }
-
-      values.replace clean_values
-    end
-    tsv
+    Signor[".source/all.csv"].tsv :header_hash => '', :merge => true, :zipped => true
   end
 
   Signor.claim Signor.protein_protein, :proc do 
@@ -69,7 +59,7 @@ module Signor
 
     parser = TSV::Parser.new Signor.data
     fields = parser.fields
-    dumper = TSV::Dumper.new :key_field => "Source (UniProt/SwissProt Accession)", :fields => ["Target (Associated Gene Name)", "Effect", "Sign", "PMID"], :type => :double, :organism => Signor.organism
+    dumper = TSV::Dumper.new :key_field => "Source (UniProt/SwissProt Accession)", :fields => ["Target (Associated Gene Name)", "Effect", "Sign", "PMID"], :type => :double, :merge => true, :organism => Signor.organism
     dumper.init
     TSV.traverse parser, :into => dumper do |k,values|
       info = {}
@@ -82,12 +72,12 @@ module Signor
       res = []
       res.extend MultipleResult
 
-      info["TYPEB"].zip(info["IDB"]).zip(info["EFFECT"]).zip(info["MECHANISM"]).zip(info["PMID"]).each do |v|
-        typeb,idb,eff,mech,pmid = v.flatten
+      info["TYPEB"].zip(info["ENTITYB"]).zip(info["IDB"]).zip(info["EFFECT"]).zip(info["MECHANISM"]).zip(info["PMID"]).each do |v|
+        typeb,nameb,idb,eff,mech,pmid = v.flatten
         
         next unless typeb == "protein"
         next unless mech == "transcriptional regulation"
-        nameb = uni2name[idb]
+        nameb ||= uni2name[idb]
         next if nameb.nil?
         sign = "Unknown"
         sign = "UP" if eff.include? 'up-regulates'
@@ -133,6 +123,10 @@ module Signor
   end
 end
 
-iif Signor.tf_tg.produce.find if __FILE__ == $0
-iif Signor.phospho_sites.produce(true).find if __FILE__ == $0
+if __FILE__ == $0
+  Log.severity = 0
+  data = Signor.tf_tg.produce(true).find
+  Log.tsv data
+  #iif Signor.tf_tg.produce.find
+end
 

data/lib/rbbt/sources/tfacts.rb

@@ -141,3 +141,10 @@ if defined? Entity and defined? Gene and Entity === Gene
     end
   end
 end
+
+
+if __FILE__ == $0
+  Log.severity = 0
+  iif TFactS.tf_tg.produce.find
+end
+

data/share/install/Organism/organism_helpers.rb

@@ -121,7 +121,7 @@ file 'identifiers' do |t|
     names = values[name_pos]
 
     matches = entrez.select do |e|
-      entrez2name.include? e and (names & entrez2name[e]).any?
+      entrez2name.include?(e) && (names & entrez2name[e]).any?
     end
 
     if matches.any?
@@ -147,7 +147,7 @@ file 'identifiers' do |t|
     identifiers = identifiers.reorder(:key, ordered_fields)
   end
 
-  entrez_synonyms = Rbbt.share.databases.entrez.gene_info.find.tsv :grep => $taxs.collect{|tax| "^#{tax}"}, :key_field => 1, :fields => [4]
+  entrez_synonyms = Rbbt.share.databases.entrez.gene_info.find.tsv :grep => $taxs.collect{|tax| "^#{tax}"}, :fixed_grep => false, :key_field => 1, :fields => [4]
   entrez_synonyms.key_field = "Entrez Gene ID"
   entrez_synonyms.fields = ["Entrez Gene Name Synonyms"]
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-sources
 version: !ruby/object:Gem::Version
-  version: 3.2.1
+  version: 3.2.2
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2022-12-15 00:00:00.000000000 Z
+date: 2023-02-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util