lib/rbbt/sources/organism.rb in rbbt-sources-1.2.0 vs lib/rbbt/sources/organism.rb in rbbt-sources-2.0.0

@@ -1,20 +1,82 @@
 require 'rbbt'
 require 'rbbt/resource'
-require 'rbbt/resource/with_key'
 
 module Organism
   extend Resource
   self.pkgdir = "rbbt"
   self.subdir = "share/organisms"
 
-  ["Hsa", "Mmu", "Rno", "Sce"].each do |organism|
+  def self.installable_organisms
+    Rbbt.share.install.Organism.find.glob('???').collect{|f| File.basename(f)}
+  end
+
+
+  Organism.installable_organisms.each do |organism|
     claim Organism[organism], :rake, Rbbt.share.install.Organism[organism].Rakefile.find
 
     module_eval "#{ organism } = with_key '#{organism}'"
   end
 
+  Rbbt.claim Rbbt.software.opt.bin.liftOver, :url, "http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/liftOver"
+
+  def self.hg_build(organism)
+    require 'rbbt/sources/ensembl_ftp'
+
+    raise "Only organism 'Hsa' (Homo sapiens) supported" unless organism =~ /^Hsa/
+
+    return 'hg19' unless organism =~ /\//
+    date = organism.split("/")[1] 
+
+    release = Ensembl.releases[date]
+
+    release.sub(/.*-/,'').to_i > 54 ? 'hg19' : 'hg18'
+  end
+
+  def self.liftOver(positions, source, target)
+
+    source_hg = hg_build(source)
+    target_hg = hg_build(target)
+
+    case
+    when (source_hg == 'hg19' and target_hg == 'hg18')
+      map_url = "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg18.over.chain.gz" 
+    when (source_hg == 'hg18' and target_hg == 'hg19')
+      map_url = "http://hgdownload.cse.ucsc.edu/goldenPath/hg18/liftOver/hg18ToHg19.over.chain.gz" 
+    else
+      return positions
+    end
+
+    positions_bed = positions.collect{|position| chr, pos = position.split(":").values_at(0,1); ["chr" << chr, pos.to_i-1, pos, position] * "\t"} * "\n" + "\n"
+    new_positions = {}
+
+    TmpFile.with_file(positions_bed) do |source_bed|
+      TmpFile.with_file() do |unmapped_file|
+        TmpFile.with_file() do |map_file|
+
+
+          Open.write(map_file, Open.read(map_url))
+          new_mutations = TmpFile.with_file() do |target_bed|
+            FileUtils.chmod(755, Rbbt.software.opt.bin.liftOver.produce.find)
+            CMD.cmd("#{Rbbt.software.opt.bin.liftOver.find} '#{source_bed}' '#{map_file}' '#{target_bed}' '#{unmapped_file}'").read
+            Open.read(target_bed) do |line|
+              chr, position_alt, position, name = line.chomp.split("\t")
+              chr.sub! /chr/, ''
+
+              old_chr, old_position, *rest = name.split(":")
+              new_positions[name] = ([chr, position].concat rest) * ":"
+            end
+          end
+        end
+      end
+    end
+
+    positions.collect do |position|
+      new_positions[position]
+    end
+  end
+
   class OrganismNotProcessedError < StandardError; end
 
   def self.attach_translations(org, tsv, target = nil, fields = nil, options = {})
     Log.high "Attaching Translations for #{ org.inspect }, target #{target.inspect}, fields #{fields.inspect}"
     options = Misc.add_defaults options, :persist => true, :case_insensitive => false
@@ -51,32 +113,38 @@
         index[list].first
       end
     end
   end
 
-  def self.guess_id(org, values, identifiers = nil)
-    identifiers ||= TSV.setup(Organism.identifiers(org), :persist => true)
-    field_matches = identifiers.field_matches(values)
-    field_matches.sort_by{|field, matches| matches.uniq.length}.last
-  end
-
   def self.guess_id(org, values)
     field_matches = TSV.field_match_counts(Organism.identifiers(org).find, values)
     field_matches.sort_by{|field, count| count.to_i}.last
   end
 
-
   def self.organisms
     Dir.glob(File.join(Organism.root.find, '*')).collect{|f| File.basename(f)}
   end
 
-  def self.name(organism)
-    Organism.scientific_name(organism).read.strip
+  def self.scientific_name(organism)
+    Organism[organism]["scientific_name"].produce.read.strip
   end
 
   def self.organism(name)
     organisms.select{|organism|
-      organism == name or Organism.name(organism) =~ /#{ name }/i
+      organism == name or Organism.scientific_name(organism) =~ /#{ name }/i
     }.first
   end
 
+  def self.known_ids(name)
+    TSV::Parser.new(Organism.identifiers(name).open).all_fields
+  end
+  
+  def self.entrez_taxid_organism(taxid)
+    all_organisms = Organism.installable_organisms
+
+    all_organisms.each do |organism|
+      return organism if Organism.entrez_taxids(organism).read.split("\n").include? taxid.to_s
+    end
+
+    raise "No organism identified for taxid #{taxid}. Supported organism are: #{all_organisms * ", "}"
+  end
 end