rbbt-sources 3.1.32 → 3.1.33

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 0c4f4b556028ce477969e38d0b4a1d8a05b01305
-  data.tar.gz: 208e92cf212d96dc3333000d350e598ec45f6361
+  metadata.gz: 1bc10d05cb25aa6e8c21a838af30f8e910915411
+  data.tar.gz: 5c1443c4088a393a33513884813ef3eb9b276ff7
 SHA512:
-  metadata.gz: 1f3e8855b0a233a6d97b80193a92fd90c45e1bfefb0f5b074a4aad2ec7151d9de1dd1c1eae842a84a9f15aeb436af4b97330845ec4ee8defe03735e65de1037f
-  data.tar.gz: a3f529915268806ac18920cfea3786ec2ab906b8492f3f8d6fd7786480a07bf1b17d6b4f5963a6175a1ff231a1697e53099fda66628e5d1fea9f7d525d7cf44e
+  metadata.gz: 9c2c009324e163840751e84ec0b2eeaff7ed02588637140f26563814183ef43666c2118b92c560cf5fff56c30d9913160e0a940092b4327259f1b18d66efa7fd
+  data.tar.gz: dc09879abc9d3b1f60ff9ecc68f4a2d34da8dfbc19aa6cfcc5640d773d8412b8aa5e3a630dba0b8a8f54c1753dfd88d61c5b50bec8a94694798e0ab376a5804d

data/lib/rbbt/sources/CASCADE.rb

@@ -12,18 +12,8 @@ module CASCADE
   #self.search_paths = {}
   #self.search_paths[:default] = :lib
 
-
-  URL = 'https://bitbucket.org/asmundf/cascade'
-  CASCADE.claim CASCADE.interactions, :proc do 
-    io = nil
-    TmpFile.with_file do |tmp|
-      Misc.in_dir tmp do
-        Log.warn "Please enter bitbucket credentials to access the asmundf/cascade repo"
-        `git clone #{URL}`
-        io = Open.open("cascade/cascade.tsv")
-      end
-    end
-
+  def self.process_interactions(file)
+    io = Open.open(file)
     tsv = TSV.open(io, :merge => true, :header_hash => '')
 
     new_fields = ["ENTITYB"] + (tsv.fields - ["ENTITYB"])
@@ -36,33 +26,19 @@ module CASCADE
       values.collect{|v| v.scan(/\d+/) * ";;"}
     end
 
-    tsv.to_s
+    tsv
   end
 
-  CASCADE.claim CASCADE.members, :proc do 
-    io = nil
-    TmpFile.with_file do |tmp|
-      Misc.in_dir tmp do
-        Log.warn "Please enter bitbucket credentials to access the asmundf/cascade repo"
-        `git clone #{URL}`
-        io = Open.open("cascade/cascade_translation.tsv")
-      end
-    end
-
-    tsv = TSV.open(io, :merge => true, :header_hash => '', :type => :flat, :sep2 => /[,.]\s*/)
-
+  def self.process_members(file)
+    TSV.open(file, :merge => true, :header_hash => '', :type => :flat, :sep2 => /[,.]\s*/)
   end
 
-  CASCADE.claim CASCADE.paradigm, :proc do
-
-    tsv = CASCADE.interactions.tsv 
-    members = CASCADE.members.tsv 
-
+  def self.process_paradigm(interactions, members)
     proteins = Set.new members.values.flatten.uniq
     outputs = Set.new
     associations = {}
 
-    tsv.through do |source, values|
+    interactions.through do |source, values|
       values.zip_fields.each do |target,typea,ida,databasea,typeb,idb,databaseb,effect|
         next if typea == 'gene'
 
@@ -129,24 +105,35 @@ module CASCADE
     str
   end
 
-  CASCADE.claim CASCADE["topology.sif"], :proc do
-
-    tsv = CASCADE.interactions.tsv 
-
-    str = StringIO.new
 
-    tsv.through do |source, values|
-      values.zip_fields.each do |target,typea,ida,databasea,typeb,idb,databaseb,effect|
-
-        effect_symbol = '->' 
-        effect_symbol = '-|' if effect.include? 'inhibit' 
+  URL = 'https://bitbucket.org/asmundf/cascade'
+  CASCADE.claim CASCADE.interactions, :proc do 
+    io = nil
+    TmpFile.with_file do |tmp|
+      Misc.in_dir tmp do
+        Log.warn "Please enter bitbucket credentials to access the asmundf/cascade repo"
+        `git clone #{URL}`
+        process_interactions("cascade/cascade.tsv")
+      end
+    end
+  end
 
-        str.puts [source, effect_symbol, target] * " "
+  CASCADE.claim CASCADE.members, :proc do 
+    TmpFile.with_file do |tmp|
+      Misc.in_dir tmp do
+        Log.warn "Please enter bitbucket credentials to access the asmundf/cascade repo"
+        `git clone #{URL}`
+        process_members("cascade/cascade_translation.tsv")
       end
     end
+  end
 
-    str.rewind
-    str
+  CASCADE.claim CASCADE.paradigm, :proc do
+
+    interactions = CASCADE.interactions.tsv 
+    members = CASCADE.members.tsv 
+
+    process_paradigm(interactions, members)
   end
 
   CASCADE.claim CASCADE.output_nodes, :proc do
@@ -173,5 +160,5 @@ iif CASCADE.interactions.produce.find if __FILE__ == $0
 iif CASCADE.members.produce.find if __FILE__ == $0
 iif CASCADE.paradigm.produce.find if __FILE__ == $0
 iif CASCADE["topology.sif"].produce.find if __FILE__ == $0
-iif CASCADE.output_nodes.produce(true).find if __FILE__ == $0
+iif CASCADE.output_nodes.produce.find if __FILE__ == $0
 

data/lib/rbbt/sources/MCLP.rb

@@ -21,5 +21,5 @@ module MCLP
   end
 end
 
-iif MCLP.RPPA.produce(true).find if __FILE__ == $0
+iif MCLP.RPPA.produce.find if __FILE__ == $0
 

data/lib/rbbt/sources/go.rb

@@ -6,7 +6,6 @@ require 'rbbt/persist/tsv'
 # now all it does is provide a translation form id to the actual names.
 module GO
 
-  extend Resource
   
   extend Resource
   self.subdir = 'share/databases/GO'
@@ -270,4 +269,3 @@ if defined? Entity
   end
 end
 
-

data/share/install/Organism/organism_helpers.rb

@@ -32,6 +32,10 @@ $biomart_transcript = [
   $biomart_ensembl_gene
 ]
 
+$biomart_transcript_cds = [
+  ['CDS Start','cdna_coding_start'],
+]
+
 $biomart_transcript_sequence = [
   ['cDNA','cdna'],
 ]
@@ -209,6 +213,12 @@ file 'transcripts' => 'gene_positions' do |t|
   Misc.sensiblewrite(t.name, transcripts.to_s)
 end
 
+file 'transcript_cds' do |t|
+  cds = BioMart.tsv($biomart_db, $biomart_ensembl_transcript, $biomart_transcript_cds, [], nil, :type => :single, :namespace => Thread.current['namespace'], :cast => :to_i)
+
+  Misc.sensiblewrite(t.name, cds.to_s)
+end
+
 file 'gene_positions' do |t|
   sequences = BioMart.tsv($biomart_db, $biomart_ensembl_gene, $biomart_gene_positions, [])
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-sources
 version: !ruby/object:Gem::Version
-  version: 3.1.32
+  version: 3.1.33
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-08-03 00:00:00.000000000 Z
+date: 2019-02-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util