rbbt-phgx 0.1.0 → 0.2.0

data/share/install/HPRD/Rakefile

@@ -0,0 +1,15 @@
+require File.join(File.dirname(__FILE__),'../lib/rake_helper')
+
+
+file :protein_protein do |t|
+  begin
+    tsv = PhGx.share.hprd["BINARY_PROTEIN_PROTEIN_INTERACTIONS.txt"].tsv :merge => true
+  rescue
+    raise "File BINARY_PROTEIN_PROTEIN_INTERACTIONS.txt not found in 'share/hprd', download manually from http://www.hprd.org/"
+  end
+  tsv.key_field = "Associated Gene Name 1"
+  tsv.fields = ["HPRD id 1","RefSeq Protein ID 1","Associated Gene Name 2","HPRD id 2","RefSeq Protein ID 2", "Experiment type", "PMID"]
+  tsv.namespace = "Hsa"
+
+  Open.write(t.name, tsv.to_s)
+end

data/share/install/KEGG/Rakefile

@@ -6,7 +6,7 @@ define_source_tasks  "h.sapiens" => "ftp://ftp.genome.jp/pub/kegg/genes/organism
   "pathways" => "ftp://ftp.genome.jp/pub/kegg/pathway/pathway"
 
 
-file :genes => 'source/h.sapiens' do |t|
+file :identifiers => 'source/h.sapiens' do |t|
   pairs = {}
   entry = nil
   Open.read(t.prerequisites.first).each do |line|
@@ -93,12 +93,12 @@ file :pathways => 'source/pathways' do |t|
     end
   end
   
-  Open.write(t.name, ['#KEGG Pathway ID', 'Name', 'Description'] * "\t" + "\n" + names.keys.collect{|pathway| [pathway, names[pathway], descs[pathway]] * "\t"} * "\n")
+  Open.write(t.name, ['#KEGG Pathway ID', 'Pathway Name', 'Pathway Description'] * "\t" + "\n" + names.keys.collect{|pathway| [pathway, names[pathway], descs[pathway]] * "\t"} * "\n")
 end
 
 process_tsv :gene_pathway, 'hsa_gene_map.tab',
   :sep2 => ' ' do 
-  headers ['KEGG Gene ID', 'KEGG Pathways']
+  headers ['KEGG Gene ID', 'KEGG Pathway ID']
   data do |gene, pathway|
     "hsa:#{ gene }\t#{pathway.flatten.collect{|name| "hsa" + name} * "|"}"
   end

data/share/install/Matador/Rakefile

@@ -4,9 +4,9 @@ define_source_tasks "matador" => "http://matador.embl.de/media/download/matador.
 
 
 process_tsv :protein_drug, 'matador',
-  :native  => 3, 
+  :key  => 3, 
   :fix     => lambda{|l| l.sub(/9606./,'')}, 
-  :extra   => [1,0,7,8,9,10,11,12], 
+  :fields   => [1,0,7,8,9,10,11,12], 
   :header_hash => "",
   :keep_empty => true do 
 

data/share/install/NCI/Rakefile

@@ -62,7 +62,7 @@ file :gene_drug => 'source/gene_drug' do |t|
   end
 
   File.open(t.name, 'w') do |f|
-    f.puts "#" + ['Associated Gene Name', 'Drugs', 'Drug Concepts', 'Statements', 'PMIDS'] * "\t"
+    f.puts "#" + ['Associated Gene Name', 'Drugs', 'Drug Concepts', 'Drug Statements', 'Drug PMIDS'] * "\t"
     info.each do |entry, line|
       f.puts line
     end
@@ -126,7 +126,7 @@ file :gene_cancer => 'source/cancer_gene' do |t|
   end
 
   File.open(t.name, 'w') do |f|
-    f.puts "#" + ['Associated Gene Name', 'Diseases', 'Disease Concepts', 'Statements', 'PMIDS'] * "\t"
+    f.puts "#" + ['Associated Gene Name', 'Diseases', 'Disease Concepts', 'Disease Statements', 'Disease PMIDS'] * "\t"
     info.each do |entry, line|
       f.puts line
     end

data/share/install/PharmaGKB/Rakefile

@@ -14,7 +14,7 @@ process_tsv :diseases, 'diseases',
   headers ['PhGKB Disease ID']
 end
 
-process_tsv :genes, 'genes', 
+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']
@@ -22,27 +22,29 @@ end
 
 process_tsv :drugs, 'drugs', 
   :header_hash => "",
-  :extra => ['Name', 'DrugBank Id'],
+  :fields => ['Name', 'Cross References'],
   :fix => proc{|l| l.gsub(/","/,'|').gsub(/"/,'').gsub(/,(\t|$)/,'\1')} do
-  headers ['PhGKB Drug ID', 'Name', 'DrugBank ID', ]
+  headers ['PhGKB Drug ID', 'Drug Name', 'Cross References', ]
 end
 
 
 process_tsv :gene_drug, 'relationships',
   :select => proc{|l| l =~ /Gene:/ && l =~ /Drug:/}, 
-  :native => 'Entity1_id', 
-  :extra => ['Entity2_id','Relationship'], 
+  :key => 'Entity1_id', 
+  :fields => ['Entity2_id','Relationship'], 
   :header_hash => "",
-  :fix => proc{|l| l.gsub(/Gene:|Drug:|Disease/,'')},
+  :merge => true,
+  :fix => proc{|l| l.gsub(/Gene:|Drug:|Disease:/,'')},
   :keep_empty => true do
 
-  headers ['PhGKB Gene ID', 'Drug']
+  headers ['PhGKB Gene ID', 'Drug Name', "Relationship"]
 end
 
 process_tsv :gene_disease, 'relationships', 
   :select => proc{|l| l =~ /Gene:/ && l =~ /Disease:/}, 
-  :native => 1, 
-  :extra => 3, 
+  :key => 1, 
+  :fields => 3, 
+  :merge => true,
   :header_hash => "",
   :fix => proc{|l| l.gsub(/Gene:|Drug:|Disease/,'')},
   :keep_empty => true do
@@ -51,18 +53,19 @@ process_tsv :gene_disease, 'relationships',
 end
 
 process_tsv :variants, 'variants', 
-  :native => 1, 
-  :extra => [3,7,8,9,10,4,5], 
+  :key => 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', 'Evidence']
+  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','Name','Source'] * "\t"
+    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"
@@ -87,7 +90,7 @@ file :gene_pathway => 'source/pathways' do |t|
   end
 
   File.open(t.name, 'w') do |f|
-    f.puts "#" + ['Pathway ID',  'Name',  'Associated Gene Name'] * "\t"
+    f.puts "#" + ['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] * "|"}"

data/share/install/Pina/Rakefile

@@ -0,0 +1,16 @@
+require File.join(File.dirname(__FILE__),'../lib/rake_helper')
+
+define_source_tasks  "Homo sapiens-20110225.txt" => "http://csbi.ltdk.helsinki.fi/pina/download/Homo%20sapiens-20110225.txt"
+
+process_tsv :protein_protein, 'Homo sapiens-20110225.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/Reactome/Rakefile

@@ -0,0 +1,36 @@
+require File.join(File.dirname(__FILE__),'../lib/rake_helper')
+
+define_source_tasks  "human_ppi" => "http://www.genomeknowledge.org/download/current/homo_sapiens.interactions.txt.gz",
+  "protein_pathway" => "http://www.genomeknowledge.org/download/current/uniprot_2_pathways.stid.txt",
+  "pathway_genesets" => "http://www.genomeknowledge.org/download/current/ReactomePathways.gmt.zip"
+
+process_tsv :protein_protein, 'human_ppi',
+  :key         => 0, 
+  :fix         => lambda{|l| l.gsub(/\t[a-z ]+:/i,"\t").gsub(/^[a-z ]+:/i,'')}, 
+  :fields      => [3,6,7,8], 
+  :header_hash => "#",
+  :merge       => true,
+  :keep_empty  => true do 
+
+  headers ['UniProt/SwissProt Accession', 'Interactor UniProt/SwissProt Accession', 'Interaction Type', 'Reactions Involved', 'Interaction PMIDS']
+end
+
+process_tsv :protein_pathway, 'protein_pathway',
+  :key         => 0, 
+  :fix         => lambda{|l| l.gsub(/\t[a-z ]+:/i,"\t").gsub(/^[a-z ]+:/i,'')}, 
+  :fields      => [1,2], 
+  :header_hash => "#",
+  :merge       => true,
+  :keep_empty  => true do 
+
+  headers ['UniProt/SwissProt Accession', 'Pathway ID', 'Pathway Description']
+end
+
+process_tsv :pathway_genesets, 'pathway_genesets',
+  :key         => 0, 
+  :fix         => lambda{|l| parts = l.split("\t"); [parts[0], parts[2..-1] * "|"] * "\t"}, 
+  :keep_empty  => true do 
+
+  headers ['Reactome Pathway Name', 'Associated Gene Name']
+end
+

data/share/install/STITCH/Rakefile

@@ -4,27 +4,27 @@ define_source_tasks "protein_chemicals" => "http://stitch.embl.de:8080/download/
   "chemicals" => "http://stitch.embl.de:8080/download/chemical.aliases.v2.0.tsv.gz"
 
 process_tsv :protein_chemical, 'protein_chemicals',
-  :native => 1,
+  :key => 1,
   :grep => "9606\.", 
   :fix => lambda{|l| l.sub(/9606\./,'')},
   :keep_empty => true do
 
-  headers ['Ensembl Protein ID', 'Chemical', 'Score']
+  headers ['Ensembl Protein ID', 'STITCH Chemical ID', 'Score']
 end
 
 $grep_re = []
 process_tsv :chemicals, 'chemicals',
   :grep => $grep_re, 
-  :native => 0 do
+  :key  => 0 do
 
   Rake::Task['protein_chemical'].invoke
 
   Log.debug "Getting chemicals"
-  chemicals = TSV.new('protein_chemical', :native => 1, :other => []).keys
+  chemicals = TSV.new('protein_chemical', :key => 1, :fields => []).keys
   Log.debug "Getting chemicals [done]"
 
   $grep_re.replace chemicals
 
-  headers ['Ensembl Protein ID', 'Chemical', 'Score']
+  headers ['STITCH Chemical ID', 'Name', 'Source']
 end
 

data/share/install/STRING/Rakefile

@@ -2,7 +2,7 @@ require File.join(File.dirname(__FILE__),'../lib/rake_helper')
 
 define_source_tasks "protein_protein" => "http://string-db.org:8080/newstring_download/protein.links.v8.3.txt.gz"
 
-process_tsv :protein_protein, 'protein_protein', :grep => '9606\.ENSP', :fix => lambda{|l| l.gsub(/9606\./,'')} do 
-  headers ['Ensembl Protein ID', 'Ensembl Protein ID', 'Score']
+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
 

data/test/rbbt/mutation/test_fireDB.rb

@@ -0,0 +1,14 @@
+require File.join(File.expand_path(File.dirname(__FILE__)), '../..', 'test_helper.rb')
+require 'rbbt/mutation/fireDB'
+
+class TestFireDB < Test::Unit::TestCase
+  def test_true
+    assert true
+    #accession = "A6NFZ4"
+    #sequence = "MAKMFDLRTKIMIGIGSSLLVAAMVLLSVVFCLYFKVAKALKAAKDPDAVAVKNHNPDKVCWATNSQAKATTMESCPSLQCCEGCRMHASSDSLPPCCCDINEGL"
+    #mutation = "Y34D"
+
+    #puts FireDB.predict(accession, sequence, mutation)
+  end
+end
+

data/test/rbbt/mutation/test_polyphen.rb

@@ -0,0 +1,20 @@
+require File.join(File.expand_path(File.dirname(__FILE__)), '../..', 'test_helper.rb')
+require 'rbbt/mutation/polyphen'
+
+class TestPolyphen2 < Test::Unit::TestCase
+  def test_predict_disease
+    accession = "A6NFZ4"
+    mutation =  "Y34D"
+
+    puts Polyphen2.predict(accession, mutation)
+  end
+
+  def test_batch
+    query =<<-EOF
+A6NFZ4 Y34D
+    EOF
+
+    puts Polyphen2::Batch.predict(query)
+  end
+end
+

data/test/rbbt/mutation/test_sift.rb

@@ -0,0 +1,23 @@
+require File.join(File.expand_path(File.dirname(__FILE__)), '../..', 'test_helper.rb')
+require 'rbbt/mutation/sift'
+
+class TestSIFT < Test::Unit::TestCase
+
+  def test_predict_aminoacid_mutation
+    accession = "NP_001008502"
+    mutation =  "Q554P"
+
+    assert_equal "TOLERATED", SIFT.predict_aminoacid_mutation(accession, mutation)[3]
+  end
+
+  def test_predict_aminoacid_mutation_batch
+    accession = "NP_001008502"
+    mutation =  "Q554P"
+
+    ddd SIFT.predict_aminoacid_mutation_batch( [[accession, mutation]])
+    assert_equal "TOLERATED", SIFT.predict_aminoacid_mutation_batch( [[accession, mutation]]).first[3]
+  end
+
+
+end
+

data/test/rbbt/mutation/test_snps_and_go.rb

@@ -0,0 +1,32 @@
+require File.join(File.expand_path(File.dirname(__FILE__)), '../..', 'test_helper.rb')
+require 'rbbt/mutation/snps_and_go'
+
+class TestSNPSandGO < Test::Unit::TestCase
+  def test_parse_mutation
+    assert_equal ['Y','233','W'], SNPSandGO.parse_mutation('Y233W')
+  end
+
+  def test_predict_disease
+    accession = "Q9UGJ1"
+    mutation =  "G1556E"
+
+    assert_raise Exception do SNPSandGO.predict(accession, mutation) end
+  end
+
+  def test_predict_disease
+    accession = "A6NFZ4"
+    mutation =  "Y34D"
+
+    assert_equal ["Disease", "2"], SNPSandGO.predict(accession, mutation)
+  end
+
+  def test_predict_neutral
+    accession = "A6NGY1"
+    mutation =  "G155R"
+
+    assert_equal ["Neutral", "9"], SNPSandGO.predict(accession, mutation)
+  end
+
+
+end
+

data/test/rbbt/sources/test_cancer.rb

@@ -5,7 +5,7 @@ require 'rbbt/sources/cancer'
 
 class TestCancer < Test::Unit::TestCase
   def test_anais_annotations
-    assert TSV.new(Cancer.anais_annotations)['ENSG00000087460']['Tumor Type'].include? 'Adrenocortical'
+    assert Cancer.anais_annotations.tsv['ENSG00000087460']['Tumor Type'].include? 'Adrenocortical'
   end
 end
 

data/test/rbbt/sources/test_matador.rb

@@ -1,11 +1,10 @@
 require File.expand_path(File.dirname(__FILE__) + '/../../test_helper')
 require 'test/unit'
-require 'rbbt/util/tmpfile'
 require 'rbbt/sources/matador'
 
 class TestMatador < Test::Unit::TestCase
-  def test_matador
-    assert_equal 'procainamide', TSV.new(Matador.protein_drug)['ENSP00000343023']['Chemical'].first
+ def test_matador
+    assert_equal 'procainamide', Matador.protein_drug.tsv['ENSP00000343023']['Chemical'].first
   end
 end
 

data/test/rbbt/sources/test_pharmagkb.rb

@@ -5,7 +5,7 @@ require 'rbbt/sources/pharmagkb'
 
 class TestPhGKB < Test::Unit::TestCase
   def test_phgkb
-    assert TSV.new(PharmaGKB.variants)['rs25487']['Associated Gene Name'].include? 'XRCC1'
+    assert PharmaGKB.variants.tsv['rs25487']['Associated Gene Name'].include? 'XRCC1'
   end
 end
 

data/test/rbbt/sources/test_stitch.rb

@@ -5,7 +5,9 @@ require 'rbbt/sources/stitch'
 
 class TestSTITCH < Test::Unit::TestCase
   def test_stitch
-    assert TSV.new(STITCH.chemicals).keys.any?
+    assert true
+    # This takes to long...
+    #assert STITCH.chemicals.tsv.keys.any?
   end
 end
 

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: rbbt-phgx
 version: !ruby/object:Gem::Version 
-  hash: 27
+  hash: 23
   prerelease: false
   segments: 
   - 0
-  - 1
+  - 2
   - 0
-  version: 0.1.0
+  version: 0.2.0
 platform: ruby
 authors: 
 - Miguel Vazquez
@@ -15,10 +15,23 @@ autorequire:
 bindir: bin
 cert_chain: []
 
-date: 2010-12-10 00:00:00 +01:00
+date: 2011-07-05 00:00:00 +02:00
 default_executable: 
-dependencies: []
-
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: rbbt-util
+  prerelease: false
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        hash: 3
+        segments: 
+        - 0
+        version: "0"
+  type: :runtime
+  version_requirements: *id001
 description: Pharmaco-genomics related data sources
 email: miguel.vazquez@fdi.ucm.es
 executables: []
@@ -30,24 +43,46 @@ extra_rdoc_files:
 files: 
 - LICENSE
 - lib/phgx.rb
+- lib/rbbt/mutation/fireDB.rb
+- lib/rbbt/mutation/polyphen.rb
+- lib/rbbt/mutation/sift.rb
+- lib/rbbt/mutation/snps_and_go.rb
+- lib/rbbt/sources/biogrid.rb
 - lib/rbbt/sources/cancer.rb
+- lib/rbbt/sources/dbsnp.rb
+- lib/rbbt/sources/hprd.rb
 - lib/rbbt/sources/kegg.rb
 - lib/rbbt/sources/matador.rb
 - lib/rbbt/sources/nci.rb
 - lib/rbbt/sources/pharmagkb.rb
+- lib/rbbt/sources/pina.rb
+- lib/rbbt/sources/reactome.rb
+- lib/rbbt/sources/sift.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/HPRD/Rakefile
 - share/install/KEGG/Rakefile
 - share/install/Matador/Rakefile
 - share/install/NCI/Rakefile
 - share/install/PharmaGKB/Rakefile
+- share/install/Pina/Rakefile
+- share/install/Reactome/Rakefile
 - share/install/STITCH/Rakefile
 - share/install/STRING/Rakefile
 - share/install/lib/rake_helper.rb
-- test/rbbt/sources/test_cancer.rb
 - test/rbbt/sources/test_matador.rb
 - test/rbbt/sources/test_pharmagkb.rb
 - test/rbbt/sources/test_stitch.rb
+- test/rbbt/sources/test_cancer.rb
+- test/rbbt/mutation/test_snps_and_go.rb
+- test/rbbt/mutation/test_fireDB.rb
+- test/rbbt/mutation/test_sift.rb
+- test/rbbt/mutation/test_polyphen.rb
 - test/test_helper.rb
 has_rdoc: true
 homepage: http://github.com/mikisvaz/rbbt-phgx
@@ -84,8 +119,12 @@ signing_key:
 specification_version: 3
 summary: Pharmaco-genomics for the Ruby Bioinformatics Toolkit (rbbt)
 test_files: 
-- test/rbbt/sources/test_cancer.rb
 - test/rbbt/sources/test_matador.rb
 - test/rbbt/sources/test_pharmagkb.rb
 - test/rbbt/sources/test_stitch.rb
+- test/rbbt/sources/test_cancer.rb
+- test/rbbt/mutation/test_snps_and_go.rb
+- test/rbbt/mutation/test_fireDB.rb
+- test/rbbt/mutation/test_sift.rb
+- test/rbbt/mutation/test_polyphen.rb
 - test/test_helper.rb