rbbt-sources 3.0.10 → 3.0.11

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: f78a7304ea51ad65f099f9982fe51527560e4fb1
-  data.tar.gz: 5eeb5990655f12c33a809f8fefa17c0efc19a799
+  metadata.gz: 50fb25a49bcb8eb484852db15e30ae3fc66c933e
+  data.tar.gz: 58ae0bb2aff4eb3f1776fb5a5b403aa14f7803c4
 SHA512:
-  metadata.gz: 791e9398599030e5f0570f87d281d5b6676b683b0e1f11a0f721e1c415ee219aa7b9a6e5b308d31f1848b24a25021ec3f582f1ce553628cd78c6b25b624f99c1
-  data.tar.gz: c499316bdf18302ab9bb9f49afb514848606f46e9b6a84536f17ae9c28ad1019fefb2638c7a41ee2e308b41ab7133e2e2c5a84a09323f9395d0afd64db1fd94c
+  metadata.gz: 8bb383dac78af82b81515f29f9e8672bda18bc607b3caa0aba54a1a0b93e90669e903cc12bc2f0d7a2ef63c31827d6c88e71b863ac98f13631fd4459a800e566
+  data.tar.gz: 506c293e96504a23e2f1f6f4ef036e1ba17a4d428e2fab814a82ba65be0c1724940a1e03fa45f245476564019504f12edde2fe7638eb1f37cd70b32a3cdabf6b

data/etc/organisms

@@ -0,0 +1 @@
+Hsa

data/lib/rbbt/sources/organism.rb

@@ -6,10 +6,24 @@ module Organism
   self.pkgdir = "rbbt"
   self.subdir = "share/organisms"
 
-  def self.installable_organisms
+  def self.organism_codes(organism = nil)
+    if organism
+      Rbbt.etc.allowed_biomart_archives.list.collect{|build| [organism, build] * "/" }
+    else
+      Rbbt.etc.organisms.list.collect{|organism|
+        organism =~ /\// ? organism : Rbbt.etc.allowed_biomart_archives.list.collect{|build| [organism, build] * "/" }
+      }.flatten.compact.uniq
+    end
+  end
+
+  def self.installed_organisms
     Rbbt.share.install.Organism.find.glob('???').collect{|f| File.basename(f)}
   end
 
+  def self.installable_organisms
+    self.installed_organisms
+  end
+
   def self.allowed_biomart_archives
     Rbbt.etc.allowed_biomart_archives.exists? ? 
       Rbbt.etc.allowed_biomart_archives.list :
@@ -29,12 +43,19 @@ module Organism
 
     raise "Only organism 'Hsa' (Homo sapiens) supported" unless organism =~ /^Hsa/
 
-    return 'hg19' unless organism =~ /\//
+    return 'hg20' unless organism =~ /\//
     date = organism.split("/")[1] 
 
     release = Ensembl.releases[date]
 
-    release.sub(/.*-/,'').to_i > 54 ? 'hg19' : 'hg18'
+    release_number = release.sub(/.*-/,'').to_i
+    if release_number <= 54 
+      'hg18'
+    elsif release_number <= 70
+      'hg19'
+    else
+      'hg20'
+    end
   end
 
   def self.liftOver(positions, source, target)

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-sources
 version: !ruby/object:Gem::Version
-  version: 3.0.10
+  version: 3.0.11
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-07-17 00:00:00.000000000 Z
+date: 2014-07-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util
@@ -88,6 +88,7 @@ extra_rdoc_files: []
 files:
 - etc/allowed_biomart_archives
 - etc/biomart/missing_in_archive
+- etc/organisms
 - lib/rbbt/sources/COSTART.rb
 - lib/rbbt/sources/CTCAE.rb
 - lib/rbbt/sources/HPRD.rb