rbbt-phgx 2.1.2 → 3.0.0

checksums.yaml

@@ -1,15 +1,7 @@
 ---
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-  metadata.gz: !binary |-
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+SHA1:
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+  data.tar.gz: 95a9925f8c9c79c2ea65e1effe28964d3ece20d8
 SHA512:
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+  data.tar.gz: 5c1f9ca7ce18f225aa5a8c013067f3e665a26c97284922e7138b22b29ef7d913b92f1a871c9b38a7c73eef4bbf0a814260d60e8ebae63b3d9d984b016c731780

metadata

@@ -1,30 +1,31 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-phgx
 version: !ruby/object:Gem::Version
-  version: 2.1.2
+  version: 3.0.0
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-11-20 00:00:00.000000000 Z
+date: 2014-02-25 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 4.0.0
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 4.0.0
-description: Pharmaco-genomics related data sources
+description: Pharmaco-genomics related data sources. Deprecated. Relevant files moved
+  to rbbt-sources for the time been
 email: miguel.vazquez@fdi.ucm.es
 executables: []
 extensions: []
@@ -43,24 +44,13 @@ files:
 - lib/rbbt/sources/biogrid.rb
 - lib/rbbt/sources/cancer.rb
 - lib/rbbt/sources/dbsnp.rb
-- lib/rbbt/sources/kegg.rb
-- lib/rbbt/sources/matador.rb
-- lib/rbbt/sources/pharmagkb.rb
-- lib/rbbt/sources/pina.rb
-- lib/rbbt/sources/stitch.rb
-- lib/rbbt/sources/string.rb
 - share/Cancer/anais_annotations
 - share/Cancer/anais_interactions
 - share/Cancer/cancer_genes.tsv
 - share/install/Biogrid/Rakefile
 - share/install/DBSNP/Rakefile
-- share/install/KEGG/Rakefile
 - share/install/Matador/Rakefile
 - share/install/NCI/Rakefile
-- share/install/PharmaGKB/Rakefile
-- share/install/Pina/Rakefile
-- share/install/STITCH/Rakefile
-- share/install/STRING/Rakefile
 - share/install/lib/rake_helper.rb
 - test/rbbt/mutation/test_chasm.rb
 - test/rbbt/mutation/test_fireDB.rb
@@ -86,32 +76,32 @@ require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.2.0
+rubygems_version: 2.2.1
 signing_key: 
 specification_version: 4
-summary: Pharmaco-genomics for the Ruby Bioinformatics Toolkit (rbbt)
+summary: DEPRECATED -- Pharmaco-genomics for the Ruby Bioinformatics Toolkit (rbbt)
 test_files:
-- test/rbbt/sources/test_matador.rb
-- test/rbbt/sources/test_cancer.rb
-- test/rbbt/sources/test_stitch.rb
-- test/rbbt/sources/test_pharmagkb.rb
-- test/rbbt/sources/test_kegg.rb
-- test/rbbt/mutation/test_oncodriveFM.rb
-- test/rbbt/mutation/test_polyphen.rb
 - test/rbbt/mutation/test_chasm.rb
-- test/rbbt/mutation/test_sift.rb
 - test/rbbt/mutation/test_transFIC.rb
 - test/rbbt/mutation/test_snps_and_go.rb
+- test/rbbt/mutation/test_sift.rb
+- test/rbbt/mutation/test_oncodriveFM.rb
+- test/rbbt/mutation/test_polyphen.rb
 - test/rbbt/mutation/test_mutation_assessor.rb
 - test/rbbt/mutation/test_fireDB.rb
+- test/rbbt/sources/test_pharmagkb.rb
+- test/rbbt/sources/test_kegg.rb
+- test/rbbt/sources/test_matador.rb
+- test/rbbt/sources/test_cancer.rb
+- test/rbbt/sources/test_stitch.rb
 - test/test_helper.rb

data/lib/rbbt/sources/kegg.rb

@@ -1,127 +0,0 @@
-require 'rbbt'
-require 'rbbt/resource'
-
-module KEGG
-  extend Resource
-  self.pkgdir = "phgx"
-  self.subdir = "share/kegg"
-
-
-  KEGG.claim KEGG.root, :rake, Rbbt.share.install.KEGG.Rakefile.find(:lib)
-
-  def self.names
-    @@names ||= KEGG.pathways.tsv :fields => ["Pathway Name"], :persist => true, :type => :single, :unnamed => true
-  end
-
-  def self.descriptions
-    @@descriptions ||= KEGG.pathways.tsv(:fields => ["Pathway Description"], :persist => true, :type => :single, :unnamed => true)
-  end
-
-
-  def self.index2genes
-    @@index2genes ||= KEGG.gene_pathway.tsv(:key_field => "KEGG Pathway ID", :fields => ["KEGG Gene ID"], :persist => true, :type => :flat, :merge => true)
-  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.name2id(name)
-    names.select{|id,n| n.downcase.index(name.downcase) == 0}.collect{|id,n| id} rescue []
-  end
-
-
-  def self.description(id)
-    descriptions[id]
-  end
-end
-
-if defined? Entity 
-
-  module KeggPathway
-    extend Entity
-    self.format = "KEGG Pathway ID"
-
-    self.annotation :organism
-
-    def self.filter(query, field = nil, options = nil, entity = nil)
-      return true if query == entity
-
-      return true if KeggPathway.setup(entity.dup, options.merge(:format => field)).name.index query
-
-      false
-    end
-
-    property :name => :single2array do
-      return nil if self.nil?
-      name = KEGG.id2name(self)
-      name.sub(/ - Homo.*/,'') unless name.nil?
-    end
-
-    property :description => :single2array do
-      KEGG.description(self)
-    end
-
-    property :genes => :array2single do |*args|
-      organism = args.first || self.organism
-      KEGG.index2genes.values_at(*self).
-        each{|gene| gene.organism = organism if gene.respond_to? :organism }
-    end
-  end
-
-  if defined? Gene and Entity === Gene
-    module Gene
-      self.format = "KEGG Gene ID"
-
-      def to_kegg
-        return self if format == "KEGG Gene ID"
-        if Array === self
-          Gene.setup(KEGG.index2kegg.values_at(*to("Ensembl Gene ID")), "KEGG Gene ID", organism).tap{|o| o.extend AnnotatedArray if AnnotatedArray === self }
-        else
-          Gene.setup(KEGG.index2kegg[to("Ensembl Gene ID")], "KEGG Gene ID", organism).tap{|o| o.extend AnnotatedArray if AnnotatedArray === self }
-        end
-      end
-
-      def from_kegg
-        return self unless format == "KEGG Gene ID"
-        if Array === self
-          Gene.setup(KEGG.index2ens.values_at(*self), "Ensembl Gene ID", organism).tap{|o| o.extend AnnotatedArray if AnnotatedArray === self }
-        else
-          Gene.setup(KEGG.index2ens[self], "Ensembl Gene ID", organism).tap{|o| o.extend AnnotatedArray if AnnotatedArray === self }
-        end
-      end
-
-      def self.gene_kegg_pathway_index
-        @@gene_kegg_pathway_index ||= 
-          KEGG.gene_pathway.tsv(:persist => true, :key_field => "KEGG Gene ID", :fields => ["KEGG Pathway ID"], :type => :flat, :merge => true)
-      end
-
-      property :to => :array2single do |new_format|
-        case
-        when format == new_format
-          self 
-        when format == "KEGG Gene ID"
-          ensembl = from_kegg.clean_annotations
-          Gene.setup(Translation.job(:tsv_translate, "", :organism => organism, :genes => ensembl, :format => new_format).exec.chunked_values_at(ensembl), new_format, organism).tap{|o| o.extend AnnotatedArray if AnnotatedArray === self }
-        when new_format == "KEGG Gene ID"
-          to_kegg
-        else
-          Gene.setup(Translation.job(:tsv_translate, "", :organism => organism, :genes => self, :format => new_format).exec.chunked_values_at(self), new_format, organism).tap{|o| o.extend AnnotatedArray if AnnotatedArray === self }
-        end
-      end
-
-      property :kegg_pathways => :array2single do
-        @kegg_pathways ||= Gene.gene_kegg_pathway_index.values_at(*self.to_kegg).
-          each{|pth| pth.organism = organism if pth.respond_to? :organism }.tap{|o| KeggPathway.setup(o, organism)}
-      end
-    end
-  end
-end

data/lib/rbbt/sources/matador.rb

@@ -1,9 +0,0 @@
-require 'phgx'
-
-module Matador
-  extend Resource
-  self.pkgdir = "phgx"
-  self.subdir = "share/matador"
-
-  Matador.claim Matador.root, :rake, Rbbt.share.install.Matador.Rakefile.find(:lib)
-end

data/lib/rbbt/sources/pharmagkb.rb

@@ -1,9 +0,0 @@
-require 'phgx'
-
-module PharmaGKB
-  extend Resource
-  self.pkgdir = "phgx"
-  self.subdir = "share/pharmagkb"
-
-  PharmaGKB.claim PharmaGKB.root, :rake, Rbbt.share.install.PharmaGKB.Rakefile.find(:lib)
-end

data/lib/rbbt/sources/pina.rb

@@ -1,35 +0,0 @@
-require 'phgx'
-
-module Pina
-  extend Resource
-  self.pkgdir = "phgx"
-  self.subdir = "share/pina"
-
-  Pina.claim Pina.root, :rake, Rbbt.share.install.Pina.Rakefile.find(:lib)
-end
-
-if defined? Entity and defined? Gene and Entity === Gene
-  require 'rbbt/entity/gene'
-  require 'rbbt/entity/interactor'
-  require 'rbbt/sources/PSI_MI'
-
-  module Gene
-    property :pina_interactors => :array2single do 
-      ens2uniprot = Organism.identifiers(organism).tsv :key_field => "Ensembl Gene ID", :fields => ["UniProt/SwissProt Accession"], :type => :flat, :persist => true, :unnamed => true
-      pina        = Pina.protein_protein.tsv(:persist => true, :fields => ["Interactor UniProt/SwissProt Accession", "Method", "PMID"], :type => :double, :merge => true, :unnamed => true)
-
-      int = self.ensembl.collect do |ens|
-        uniprot = ens2uniprot[ens]
-        list = pina.values_at(*uniprot).compact.collect do |v|
-          Misc.zip_fields(v).collect do |o, method, articles|
-            Interactor.setup(o, PSI_MITerm.setup(method.split(";;")), PMID.setup(articles.split(";;")))
-          end
-        end.flatten.uniq
-        Gene.setup(list, "UniProt/SwissProt Accession", organism).extend(AnnotatedArray)
-      end
-
-      Gene.setup(int, "UniProt/SwissProt Accession", organism).extend(AnnotatedArray)
-    end
-  end
-end
-

data/lib/rbbt/sources/stitch.rb

@@ -1,9 +0,0 @@
-require 'phgx'
-
-module STITCH
-  extend Resource
-  self.pkgdir = "phgx"
-  self.subdir = "share/stitch"
-
-  STITCH.claim STITCH.root, :rake, Rbbt.share.install.STITCH.Rakefile.find(:lib)
-end

data/lib/rbbt/sources/string.rb

@@ -1,27 +0,0 @@
-require 'phgx'
-
-module STRING
-  extend Resource
-  self.pkgdir = "phgx"
-  self.subdir = "share/string"
-
-  STRING.claim STRING.root, :rake, Rbbt.share.install.STRING.Rakefile.find(:lib)
-end
-
-if defined? Entity and defined? Gene and Entity === Gene
-  module Gene
-    property :string_interactors => :array2single do |*args|
-      threshold = args.first || 800
-      string = STRING.protein_protein.tsv(:unnamed => true, :persist => true, :type => :double)
-      all = self.ensembl.collect do |gene|
-        interactors = gene.proteins.collect{|protein| Misc.zip_fields((string[protein] || [[],[]])).select{|i, score| score.to_i > threshold}.collect{|ints,s| ints}}.compact.flatten.uniq
-        Protein.setup(interactors, "Ensembl Protein ID", organism).transcript.gene.compact.uniq
-      end
-
-      all.compact.first.annotate all if Annotated === all.compact.first 
-
-      all
-    end
-  end
-end
-

data/share/install/KEGG/Rakefile

@@ -1,114 +0,0 @@
-require File.join(File.dirname(__FILE__),'../lib/rake_helper')
-
-define_source_tasks  "h.sapiens" => "ftp://ftp.genome.jp/pub/kegg/genes/organisms/hsa/H.sapiens.ent",
-  "hsa_gene_map.tab" => "ftp://ftp.genome.jp/pub/kegg/pathway/organisms/hsa/hsa_gene_map.tab",
-  "drugs" => "ftp://ftp.genome.jp/pub/kegg/medicus/drug/drug",
-  "pathways" => "ftp://ftp.genome.jp/pub/kegg/pathway/pathway"
-
-
-file :identifiers => 'source/h.sapiens' do |t|
-  pairs = {}
-  entry = nil
-  Open.read(t.prerequisites.first).each do |line|
-    if line =~ /^ENTRY\s+(\d+)/
-      entry = $1
-      next
-    end
-
-    if line =~ /Ensembl: (ENSG\d+)/
-      pairs[entry] = $1
-    end
-  end
-
-  Open.write(t.name, ['#Ensembl Gene ID','KEGG Gene ID'] * "\t" + "\n" + pairs.collect{|entry, ens| [ens, "hsa:" + entry] * "\t"} * "\n")
-end
-
-file :gene_drug => 'source/drugs' do |t|
-  pairs = {}
-  drug = nil
-  Open.read(t.prerequisites.first).
-    scan(/^[A-Z].*?(?:^[A-Z])/sm).select{|line| line =~ /^ENTRY|TARGET/}.collect{|line| line.sub(/\s+/,' ')}.each do |line|
-      if line =~ /^ENTRY\s+(\w+)/
-        drug = $1
-        next
-      end
-
-      if line =~ /TARGET.*?\[HSA:(.*?)\]/
-        genes = $1.split(/\s/)
-        genes.each do |gene|
-          pairs[gene] ||= []
-          pairs[gene] << drug
-        end
-      end
-  end
-
-  Open.write(t.name, ['#KEGG Gene ID', 'KEGG Drug ID'] * "\t" + "\n" + pairs.collect{|gene, drugs| ["hsa:" + gene, drugs * "|" ] * "\t"} * "\n")
-end
-
-file :drugs => 'source/drugs' do |t|
-  info = {}
-  drug = nil
-  Open.read(t.prerequisites.first).
-    scan(/^[A-Z].*?(?:^[A-Z])/sm).select{|line| line =~ /^ENTRY|NAME|DBLINKS/}.collect{|line| line.sub(/\s+/,' ')}.each do |line|
-      if line =~ /^ENTRY\s+(\w+)/
-        drug = $1
-        next
-      end
-
-      if line =~ /^NAME(.*)/
-        names = $1.split(/;/)
-        names.each do |name|
-          info[drug] ||= [[],[]]
-          info[drug][0] << name.chomp.strip
-        end
-      end
-
-      if line =~ /^DBLINKS(.*)/
-        $1.match(/PubChem: (\d*)/)
-        pubchem = $1
-        next unless pubchem
-        info[drug] ||= [[],[]]
-        info[drug][1] << pubchem.chomp.strip
-      end
-  end
-
-  Open.write(t.name, ['#KEGG Drug ID', 'KEGG Drug Name', 'PubChem Drug ID'] * "\t" + "\n" + info.collect{|drug, info| [drug, info.collect{|v| v * "|"} ].flatten * "\t"} * "\n")
-end
-
-file :pathways => 'source/pathways' do |t|
-  descs = {}
-  names = {}
-  klass = {}
-  pathway = nil
-  Open.read(t.prerequisites.first).split(/\n/).each do |line|
-    if line =~ /ENTRY\s+(\w+)/
-      pathway = $1.strip
-    end
-
-    if line =~ /NAME (.*)/
-      names[pathway] = $1.strip
-    end
-
-    if line =~ /DESCRIPTION (.*)/
-      descs[pathway] = $1.strip
-    end
-
-    if line =~ /CLASS (.*)/
-      klass[pathway] = $1.strip
-    end
-  end
-  
-  Open.write(t.name, "#: :type=:list\n" + ['#KEGG Pathway ID', 'Pathway Name', 'Pathway Description', 'Pathway Class'] * "\t" + "\n" + names.keys.collect{|pathway| [pathway, names[pathway], descs[pathway], klass[pathway]] * "\t"} * "\n")
-end
-
-process_tsv :gene_pathway, 'hsa_gene_map.tab',
-  :sep2 => ' ' do 
-  headers ['KEGG Gene ID', 'KEGG Pathway ID']
-  data do |gene, pathway|
-    "hsa:#{ gene }\t#{pathway.flatten.collect{|name| "hsa" + name} * "|"}"
-  end
-end
-
-add_to_defaults [:pathways, :drugs, :gene_drug, :genes]
-
-

data/share/install/PharmaGKB/Rakefile

@@ -1,211 +0,0 @@
-require File.join(File.dirname(__FILE__),'../lib/rake_helper')
-
-define_source_tasks "genes" => "http://www.pharmgkb.org/commonFileDownload.action?filename=genes.zip",
-  "drugs" => "http://www.pharmgkb.org/commonFileDownload.action?filename=drugs.zip",
-  "diseases" => "http://www.pharmgkb.org/commonFileDownload.action?filename=diseases.zip",
-  "relationships" => "http://www.pharmgkb.org/commonFileDownload.action?filename=relationships.zip",
-  "variants" => "http://www.pharmgkb.org/commonFileDownload.action?filename=variantAnnotations.zip",
-  "pathways" => "http://www.pharmgkb.org/commonFileDownload.action?filename=pathways-tsv.zip"
- 
-
-process_tsv :diseases, 'diseases', 
-  :header_hash => "",
-  :fix => proc{|l| l.gsub(/","/,'|').gsub(/"/,'').gsub(/,(\t|$)/,'\1')} do
-  headers ['PhGKB Disease ID']
-end
-
-process_tsv :identifiers, 'genes', 
-  :header_hash => "",
-  :fix => proc{|l| l.gsub(/","/,'|').gsub(/"/,'').gsub(/,(\t|$)/,'\1')} do
-  headers ['PhGKB Gene ID', 'Entrez Gene ID', 'Ensembl Gene Id', 'UniProt/SwissProt Accession', 'Long Name', 'Associated Gene Name']
-end
-
-process_tsv :drugs, 'drugs', 
-  :header_hash => "",
-  :fields => ['Name', 'DrugBank Id', 'SMILES', "MeSH IDs"],
-  :fix => proc{|l| l.gsub(/","/,'|').gsub(/"/,'').gsub(/,(\t|$)/,'\1')} do
-  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:/}, 
-  :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
-
-    parts * "\t"
-  },
-  :keep_empty => true do
-
-  headers ['PhGKB Gene ID', 'PhGKB Drug ID']
-end
-
-process_tsv :gene_disease, 'relationships', 
-  :select => proc{|l| l =~ /^Gene:/ && l =~ /Disease:/}, 
-  :key_field => 1, 
-  :fields => 3, 
-  :merge => true,
-  :header_hash => "",
-  :fix => proc{|l| l.gsub(/Gene:|Drug:|Disease/,'')},
-  :keep_empty => true do
-
-  headers ['PhGKB Gene ID', 'PhGKB Disease ID']
-end
-
-process_tsv :variants, 'variants', 
-  :key_field => 1, 
-  :fields => [3,7,8,9,10,4,6,5], 
-  :header_hash => "",
-  :merge => true,
-  :fix => proc{|l| l.gsub(/Gene:|Drug:|Disease/,'')},
-  :keep_empty => true do
-
-  headers ['Variant ID', 'Associated Gene Name', 'Drug', 'Drug_Class', 'Disease', 'Curation', 'Feature', 'Annotation', 'Evidence']
-end
-
-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|
-      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
-
-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
-
-  File.open(t.name, 'w') do |f|
-    f.puts "#" + ['PhGKB Pathway ID',  'Pathway Name',  'Associated Gene Name'] * "\t"
-    pathways.each do |pathway, info|
-      next if info[:genes].nil?
-      f.puts "#{ pathway }\t#{info[:name]}\t#{info[:genes] * "|"}"
-    end
-  end
-end
-
-file :pathway_drugs => '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 =='Drug'
-      pathways[last_pathway][:drugs] ||= []
-      pathways[last_pathway][:drugs] << code
-    end
-  end
-
-  File.open(t.name, 'w') do |f|
-    f.puts "#" + ["PhGKB Pathway ID", "PhGKB Drug ID"]* "\t"
-    pathways.each do |pathway, info|
-      next if info[:drugs].nil?
-      f.puts "#{ pathway }\t#{info[:drugs] * "|"}"
-    end
-  end
-end
-
-
-file :disease_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 =='Disease'
-      pathways[last_pathway][:diseases] ||= []
-      pathways[last_pathway][:diseases] << name
-    end
-  end
-
-  File.open(t.name, 'w') do |f|
-    f.puts "#" + %w(ID Name Diseases) * "\t"
-    pathways.each do |pathway, info|
-      next if info[:diseases].nil?
-      f.puts "#{ pathway }\t#{info[:name]}\t#{info[:diseases] * "|"}"
-    end
-  end
-end
-
-add_to_defaults [:gene_pathway, :drug_pathway, :disease_pathway]

data/share/install/Pina/Rakefile

@@ -1,16 +0,0 @@
-require File.join(File.dirname(__FILE__),'../lib/rake_helper')
-
-define_source_tasks  "Homo sapiens-20110628.txt" => "http://cbg.garvan.unsw.edu.au/pina/download/Homo%20sapiens-20110628.txt"
-
-process_tsv :protein_protein, 'Homo sapiens-20110628.txt',
-  :key         => 0, 
-  :fix         => lambda{|l| l.gsub("uniprotkb:", '').gsub("(gene name)",'').gsub("pubmed:",'').gsub("|", ';;').gsub(/\([^)]+\)/,'')}, 
-  :fields      => [1,6,8], 
-  :header_hash => "#",
-  :merge       => true,
-  :keep_empty  => true do 
-
-  headers ['UniProt/SwissProt Accession', 'Interactor UniProt/SwissProt Accession', 'Method', 'PMID']
-end
-
-

data/share/install/STITCH/Rakefile

@@ -1,30 +0,0 @@
-require File.join(File.dirname(__FILE__),'../lib/rake_helper')
-
-define_source_tasks "protein_chemicals" => "http://stitch.embl.de:8080/download/protein_chemical.links.v2.0.tsv.gz",
-  "chemicals" => "http://stitch.embl.de:8080/download/chemical.aliases.v2.0.tsv.gz"
-
-process_tsv :protein_chemical, 'protein_chemicals',
-  :key => 1,
-  :grep => "9606\.", 
-  :fix => lambda{|l| l.sub(/9606\./,'')},
-  :keep_empty => true do
-
-  headers ['Ensembl Protein ID', 'STITCH Chemical ID', 'Score']
-end
-
-$grep_re = []
-process_tsv :chemicals, 'chemicals',
-  :grep => $grep_re, 
-  :key  => 0 do
-
-  Rake::Task['protein_chemical'].invoke
-
-  Log.debug "Getting chemicals"
-  chemicals = TSV.open('protein_chemical', :key_field => 1, :fields => []).keys
-  Log.debug "Getting chemicals [done]"
-
-  $grep_re.replace chemicals
-
-  headers ['STITCH Chemical ID', 'Name', 'Source']
-end
-

data/share/install/STRING/Rakefile

@@ -1,8 +0,0 @@
-require File.join(File.dirname(__FILE__),'../lib/rake_helper')
-
-define_source_tasks "protein_protein" => "http://string-db.org/newstring_download/protein.links.v9.05.txt.gz"
-
-process_tsv :protein_protein, 'protein_protein', :grep => '9606\.ENSP', :fix => lambda{|l| l.gsub(/9606\./,'')}, :merge => true, :sep => "\s" do 
-  headers ['Ensembl Protein ID', 'Interactor Ensembl Protein ID', 'Score']
-end
-