rbbt-phgx 2.0.0 → 2.0.1

data/lib/rbbt/mutation/chasm.rb

@@ -0,0 +1,79 @@
+require 'rbbt/util/open'
+require 'rbbt/tsv'
+require 'nokogiri'
+require 'digest/md5'
+require 'net/http/post/multipart'
+
+module CHASM
+
+  class NotDone < StandardError; end
+
+  URL="http://www.cravat.us/ClassifierSelect1"
+  ASTERISK = "*"[0]
+
+  # Hash of samples pointing to mutations specified in Ensembl Transcript ID
+  def self.predict(mutations_by_sample, options = {})
+    options = Misc.add_defaults options, :chosendb => "CHASM", :emailbox => 'dev@null.org', :analysistype => 'driver', :inputfile => nil
+    mutationbox = []
+    i = 1
+    mutations_by_sample.each do |sample,mutations|
+      mutations.each do |mutation|
+        mutationbox << [i, sample].concat(mutation.split(":"))
+      end
+      i += 1
+    end
+
+    options[:mutationbox] = mutationbox.collect{|line| line * "\t"} * "\n"
+    post_data = options.collect{|k,v| [k,v] * "="} * "&"
+
+    Log.debug "Querying CHASM for: #{mutationbox.length} mutations in #{mutations_by_sample.length} samples"
+
+    tries = 0
+    nocache = false
+    begin
+      doc = nil
+      TmpFile.with_file(post_data) do |post_file|
+        Log.medium "Updating cache:" if nocache == :update
+
+        url = URI.parse(URL)
+        req = Net::HTTP::Post::Multipart.new url.path, options
+        res = Net::HTTP.start(url.host, url.port) do |http|
+          http.request(req)
+        end
+        job_id = JSON.parse(res.body)["jobId"]
+        puts job_id
+      end
+    end
+  end
+
+  def self.chunked_predict(mutations, max = 1000)
+    flattened_mutations = mutations.collect{|g,list| list = [list] unless Array === list; list.collect{|m| [g,m] } }.flatten(1)
+    chunks = flattened_mutations.length.to_f / max
+    chunks = chunks.ceil
+
+    Log.debug("Mutation Assessor ran with #{chunks} chunks of #{ max } mutations") if chunks > 1
+    num = 1
+    Misc.divide(flattened_mutations, chunks).inject(nil) do |acc, list|
+      Log.debug("Mutation Assessor ran with #{chunks} chunks: chunk #{num}") if chunks > 1
+      unflattened_mutations = {}
+      list.each{|g,m| next if g.nil?; unflattened_mutations[g] ||= []; unflattened_mutations[g] << m}
+      if acc.nil?
+        acc = predict(unflattened_mutations)
+      else
+        acc = TSV.setup(acc.merge(predict(unflattened_mutations)))
+      end
+      num += 1
+      acc
+    end
+  end
+end
+
+
+__END__
+
+name="mutationbox" 1 NP_001135977 R641W 1 
+name="inputfile" 
+name="analysistype" driver
+name="chosendb" CHASM 
+name="cancertype" Breast 
+name="emailbox" mikisvaz@gmail.com

data/lib/rbbt/sources/kegg.rb

@@ -7,7 +7,7 @@ module KEGG
   self.subdir = "share/kegg"
 
 
-  KEGG.claim KEGG.root.find, :rake, Rbbt.share.install.KEGG.Rakefile.find(:lib)
+  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

data/lib/rbbt/sources/matador.rb

@@ -5,5 +5,5 @@ module Matador
   self.pkgdir = "phgx"
   self.subdir = "share/matador"
 
-  Matador.claim Matador.root.find, :rake, Rbbt.share.install.Matador.Rakefile.find(:lib)
+  Matador.claim Matador.root, :rake, Rbbt.share.install.Matador.Rakefile.find(:lib)
 end

data/lib/rbbt/sources/pina.rb

@@ -5,7 +5,7 @@ module Pina
   self.pkgdir = "phgx"
   self.subdir = "share/pina"
 
-  Pina.claim Pina.root.find, :rake, Rbbt.share.install.Pina.Rakefile.find(:lib)
+  Pina.claim Pina.root, :rake, Rbbt.share.install.Pina.Rakefile.find(:lib)
 end
 
 if defined? Entity and defined? Gene and Entity === Gene

data/lib/rbbt/sources/stitch.rb

@@ -5,5 +5,5 @@ module STITCH
   self.pkgdir = "phgx"
   self.subdir = "share/stitch"
 
-  STITCH.claim STITCH.root.find, :rake, Rbbt.share.install.STITCH.Rakefile.find(:lib)
+  STITCH.claim STITCH.root, :rake, Rbbt.share.install.STITCH.Rakefile.find(:lib)
 end

data/lib/rbbt/sources/string.rb

@@ -5,7 +5,7 @@ module STRING
   self.pkgdir = "phgx"
   self.subdir = "share/string"
 
-  STRING.claim STRING.root.find, :rake, Rbbt.share.install.STRING.Rakefile.find(:lib)
+  STRING.claim STRING.root, :rake, Rbbt.share.install.STRING.Rakefile.find(:lib)
 end
 
 if defined? Entity and defined? Gene and Entity === Gene

data/test/rbbt/mutation/test_chasm.rb

@@ -0,0 +1,14 @@
+require File.join(File.expand_path(File.dirname(__FILE__)), '../..', 'test_helper.rb')
+require 'rbbt/mutation/chasm'
+
+class TestCHASM < Test::Unit::TestCase
+
+  def test_predict_aminoacid_mutation
+    sample_mutations = {
+      "Sample_1" => ["ENST00000531739:R641W"]
+
+    }
+    ddd CHASM.predict(sample_mutations, :cancertype => "Breast")
+  end
+end
+

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-phgx
 version: !ruby/object:Gem::Version
-  version: 2.0.0
+  version: 2.0.1
   prerelease: 
 platform: ruby
 authors:
@@ -9,7 +9,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-12-21 00:00:00.000000000 Z
+date: 2013-01-09 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util
@@ -36,6 +36,7 @@ extra_rdoc_files:
 files:
 - LICENSE
 - lib/phgx.rb
+- lib/rbbt/mutation/chasm.rb
 - lib/rbbt/mutation/fireDB.rb
 - lib/rbbt/mutation/mutation_assessor.rb
 - lib/rbbt/mutation/oncodriveFM.rb
@@ -67,17 +68,18 @@ files:
 - share/install/lib/rake_helper.rb
 - share/install/software/OncodriveFM
 - 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/sources/test_stitch.rb
+- test/rbbt/sources/test_pharmagkb.rb
 - test/rbbt/sources/test_kegg.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/rbbt/mutation/test_mutation_assessor.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_mutation_assessor.rb
+- test/rbbt/mutation/test_fireDB.rb
 - test/test_helper.rb
 homepage: http://github.com/mikisvaz/rbbt-phgx
 licenses: []
@@ -105,15 +107,16 @@ specification_version: 3
 summary: Pharmaco-genomics for the Ruby Bioinformatics Toolkit (rbbt)
 test_files:
 - 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/sources/test_stitch.rb
+- test/rbbt/sources/test_pharmagkb.rb
 - test/rbbt/sources/test_kegg.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/rbbt/mutation/test_mutation_assessor.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_mutation_assessor.rb
+- test/rbbt/mutation/test_fireDB.rb
 - test/test_helper.rb