rbbt-phgx 0.3.0 → 0.3.1

data/lib/rbbt/mutation/mutation_assessor.rb

@@ -87,7 +87,7 @@ module MutationAssessor
         acc = TSV.setup(acc.merge(predict(list)))
       end
       acc
-    end || {}
+    end
   end
 
   def self.add_predictions(tsv)

data/lib/rbbt/sources/kegg.rb

@@ -7,4 +7,51 @@ module KEGG
   self.subdir = "share/kegg"
 
   KEGG.claim KEGG.root.find, :rake, Rbbt.share.install.KEGG.Rakefile.find(:lib)
+
+  def self.names
+    @@names ||= KEGG.pathways.tsv :fields => ["Pathway Name"], :persist => true, :type => :single
+  end
+
+  def self.descriptions
+    @@descriptions ||= KEGG.pathways.tsv :fields => ["Pathway Description"], :persist => true, :type => :single
+  end
+
+
+  def self.index2ens
+    @@index2ens ||= KEGG.identifiers.index :persist => true
+  end
+
+  def self.index2kegg
+    @@index2kegg ||= KEGG.identifiers.index :target => "KEGG Gene ID", :persist => true
+  end
+
+  def self.id2name(id)
+    names[id]
+  end
+
+  def self.description(id)
+    descriptions[id]
+  end
+end
+
+module Gene
+
+  def to_kegg
+    if Array === self
+      Gene.setup(KEGG.index2kegg.values_at(*to("Ensembl Gene ID")), "KEGG Gene ID", organism)
+    else
+      Gene.setup(KEGG.index2kegg[to("Ensembl Gene ID")], "KEGG Gene ID", organism)
+    end
+  end
+
+  def from_kegg
+    if Array === self
+      Gene.setup(KEGG.index2ens.values_at(*self), "Ensembl Gene ID", organism)
+    else
+      Gene.setup(KEGG.index2ens[self], "Ensembl Gene ID", organism)
+    end
+  end
+
+
+
 end

data/lib/rbbt/sources/pina.rb

@@ -2,5 +2,8 @@ require 'phgx'
 
 module Pina
   extend Resource
-  data_module PhGx
+  self.pkgdir = "phgx"
+  self.subdir = "share/pina"
+
+  Pina.claim Pina.root.find, :rake, Rbbt.share.install.Pina.Rakefile.find(:lib)
 end

data/lib/rbbt/sources/stitch.rb

@@ -2,5 +2,8 @@ require 'phgx'
 
 module STITCH
   extend Resource
-  data_module PhGx
+  self.pkgdir = "phgx"
+  self.subdir = "share/stitch"
+
+  STITCH.claim STITCH.root.find, :rake, Rbbt.share.install.STITCH.Rakefile.find(:lib)
 end

data/lib/rbbt/sources/string.rb

@@ -2,5 +2,9 @@ require 'phgx'
 
 module STRING
   extend Resource
-  data_module PhGx
+  self.pkgdir = "phgx"
+  self.subdir = "share/string"
+
+  STRING.claim STRING.root.find, :rake, Rbbt.share.install.STRING.Rakefile.find(:lib)
+
 end

data/share/install/PharmaGKB/Rakefile

@@ -22,26 +22,64 @@ end
 
 process_tsv :drugs, 'drugs', 
   :header_hash => "",
-  :fields => ['Name', 'Cross References'],
+  :fields => ['Name', 'DrugBank Id', 'SMILES', "MeSH IDs"],
   :fix => proc{|l| l.gsub(/","/,'|').gsub(/"/,'').gsub(/,(\t|$)/,'\1')} do
-  headers ['PhGKB Drug ID', 'Drug Name', 'Cross References', ]
+  headers ['PhGKB Drug ID', 'Drug Name', 'DrugBank Id', 'SMILES', "MeSH ID"]
+end
+
+process_tsv :relationships, 'relationships',
+  :header_hash => "",
+  :merge => true,
+  :fix => proc{|l| 
+    l.gsub!(/Gene:|Drug:|Disease:/,'')
+    parts = l.split("\t")
+    rels = parts.pop
+    parts = [parts.values_at(0, 2) * ":"]
+    pmids = []
+    pathways = []
+    rsids = []
+    rels.split(',').each do |r|
+      case
+      when r =~ /PMID:(.*)/
+        pmids << $1
+      when r =~ /Pathway:(.*)/
+        pathways << $1
+      when r =~ /RSID:(.*)/
+        rsids << $1
+      end
+    end
+
+    parts << pmids * "|"
+    parts << pathways * "|"
+    parts << rsids * "|"
+
+    parts * "\t"
+  },
+  :keep_empty => true do
+
+  headers ['PhGKB Relationship', "PMID", "PhGKB Pathway ID", "Variant ID"]
 end
 
 
 process_tsv :gene_drug, 'relationships',
-  :select => proc{|l| l =~ /Gene:/ && l =~ /Drug:/}, 
-  :key_field => 'Entity1_id', 
-  :fields => ['Entity2_id','Relationship'], 
+  :select => proc{|l| l =~ /^Gene:/ && l =~ /Drug:/}, 
   :header_hash => "",
   :merge => true,
-  :fix => proc{|l| l.gsub(/Gene:|Drug:|Disease:/,'')},
+  :fix => proc{|l| 
+    l.gsub!(/Gene:|Drug:|Disease:/,'')
+    parts = l.split("\t")
+    rels = parts.pop
+    parts = parts.values_at 0, 2
+
+    parts * "\t"
+  },
   :keep_empty => true do
 
-  headers ['PhGKB Gene ID', 'Drug Name', "Relationship"]
+  headers ['PhGKB Gene ID', 'PhGKB Drug ID']
 end
 
 process_tsv :gene_disease, 'relationships', 
-  :select => proc{|l| l =~ /Gene:/ && l =~ /Disease:/}, 
+  :select => proc{|l| l =~ /^Gene:/ && l =~ /Disease:/}, 
   :key_field => 1, 
   :fields => 3, 
   :merge => true,
@@ -67,8 +105,29 @@ file :pathways => 'source/pathways' do |t|
   File.open(t.name, 'w') do |f|
     f.puts "#" + ['PhGKB Pathway ID','Pathway Name','Pathway Annotation Source'] * "\t"
     Open.read(t.prerequisites.first).split(/\n/).each do |line|
-      next unless line =~ /(PA\d+): (.*) - \((.*)\)/
-      f.puts [$1,$2,$3] * "\t"
+      case
+      when line =~ /(PA\d+): (.*) - \((.*)\)/
+        f.puts [$1,$2,$3] * "\t"
+      when line =~ /(PA\d+): (.*)/
+        f.puts [$1,$2,""] * "\t"
+      end
+    end
+  end
+end
+
+file :gene_pathway => 'source/pathways' do |t|
+  pathways = {}
+  last_pathway = nil
+
+  Open.read(t.prerequisites.first).split(/\n/).each do |line|
+    if line =~ /(P.*):(.*)/
+      last_pathway = $1
+      pathways[last_pathway] = {:name => $2}
+    else
+      type, code, name = line.split(/\t/)
+      next unless type =='Gene'
+      pathways[last_pathway][:genes] ||= []
+      pathways[last_pathway][:genes] << name
     end
   end
 end
@@ -98,7 +157,7 @@ file :gene_pathway => 'source/pathways' do |t|
   end
 end
 
-file :drug_pathway => 'source/pathways' do |t|
+file :pathway_drugs => 'source/pathways' do |t|
   pathways = {}
   last_pathway = nil
 
@@ -110,15 +169,15 @@ file :drug_pathway => 'source/pathways' do |t|
       type, code, name = line.split(/\t/)
     next unless type =='Drug'
       pathways[last_pathway][:drugs] ||= []
-      pathways[last_pathway][:drugs] << name
+      pathways[last_pathway][:drugs] << code
     end
   end
 
   File.open(t.name, 'w') do |f|
-    f.puts "#" + %w(ID Name Drugs) * "\t"
+    f.puts "#" + ["PhGKB Pathway ID", "PhGKB Drug ID"]* "\t"
     pathways.each do |pathway, info|
       next if info[:drugs].nil?
-      f.puts "#{ pathway }\t#{info[:name]}\t#{info[:drugs] * "|"}"
+      f.puts "#{ pathway }\t#{info[:drugs] * "|"}"
     end
   end
 end

data/share/install/STITCH/Rakefile

@@ -20,7 +20,7 @@ process_tsv :chemicals, 'chemicals',
   Rake::Task['protein_chemical'].invoke
 
   Log.debug "Getting chemicals"
-  chemicals = TSV.new('protein_chemical', :key => 1, :fields => []).keys
+  chemicals = TSV.open('protein_chemical', :key_field => 1, :fields => []).keys
   Log.debug "Getting chemicals [done]"
 
   $grep_re.replace chemicals

data/share/install/lib/rake_helper.rb

@@ -49,8 +49,6 @@ def process_tsv(file, source, options = {}, &block)
       data_fields = d.fields.dup.unshift d.key_field
       if $__headers.nil?
         $__headers = data_fields
-      else
-       $__headers = data_fields.zip($__headers).collect{|l| l.compact.last}
       end
     end
 

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: rbbt-phgx
 version: !ruby/object:Gem::Version 
-  hash: 19
-  prerelease: false
+  hash: 17
+  prerelease: 
   segments: 
   - 0
   - 3
-  - 0
-  version: 0.3.0
+  - 1
+  version: 0.3.1
 platform: ruby
 authors: 
 - Miguel Vazquez
@@ -15,7 +15,7 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2011-09-07 00:00:00 +02:00
+date: 2011-10-03 00:00:00 +02:00
 default_executable: 
 dependencies: 
 - !ruby/object:Gem::Dependency 
@@ -118,7 +118,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
 requirements: []
 
 rubyforge_project: 
-rubygems_version: 1.3.7
+rubygems_version: 1.6.2
 signing_key: 
 specification_version: 3
 summary: Pharmaco-genomics for the Ruby Bioinformatics Toolkit (rbbt)