rbbt-sources 3.0.14 → 3.0.16

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 44c4642f4e5c392008336caa916d504c46c17216
-  data.tar.gz: e678ca8dd3a41639b1c5ad62adec658b8cf870fa
+  metadata.gz: 62838e9efa3c3cbab442302949e74407a46dbe15
+  data.tar.gz: 0c43d26fec66e78ef09d7dec5ad0d06b4502a189
 SHA512:
-  metadata.gz: f1a38cc05206dec04fb3db08c4685f0bd92e39305acfe92ede5d017ea33bc9eb98f3b542df4c8db3b78fb551b02c7d77c4f7ef7297e38ee868c38204ca8f4a85
-  data.tar.gz: 540498257d57872b85a3bc391ad697fe72cefab2228511104f074e2322e8e0815f90dbeb6d734bc1694f31cf1884d25d8303c48bc097221dadca96970689eb5b
+  metadata.gz: 72afc70a5edfe98c9bbc13efc80c3d3cde8a73167d33036cef6afa8f3afc41bc930ca3d4402308ec6545bd4ccfc9d9feb0c100967872599be1dce865f54e4022
+  data.tar.gz: 529fec12bdfc2cdae42129659600eaa5c1bec7dc95b12d0342a633334ff25163ee2f0abf7077267db19871e3a25e28be37d8b962818dfd67410fe62310b0b6e0

data/lib/rbbt/sources/organism.rb

@@ -6,6 +6,10 @@ module Organism
   self.pkgdir = "rbbt"
   self.subdir = "share/organisms"
 
+  def self.default_code(organism = "Hsa")
+    organism.split("/").first << "/feb2014"
+  end
+
   def self.organism_codes(organism = nil)
     if organism
       Rbbt.etc.allowed_biomart_archives.list.collect{|build| [organism, build] * "/" }

data/share/install/Organism/organism_helpers.rb

@@ -540,8 +540,8 @@ file 'transcript_sequence' => ["exons", "transcript_exons"] do |t|
   chr_transcript_ranges ||= {}
   transcript_strand = {}
 
-  #TSV.open('transcript_exons', :unnamed => true).through do |transcript, values|
-  TSV.traverse Path.setup(File.expand_path('transcript_exons')) do |transcript,values|
+  transcript_exons = Path.setup(File.expand_path('transcript_exons'))
+  TSV.traverse transcript_exons do |transcript,values|
     transcript = transcript.first if Array === transcript
     transcript_ranges = []
 
@@ -572,7 +572,8 @@ file 'transcript_sequence' => ["exons", "transcript_exons"] do |t|
       p.sub!(%r{.*/organisms/},'share/organisms/')
       chr_str = p.produce.read
     rescue Exception
-      Log.debug("Chr #{ chr } failed (#{transcript_ranges.length} transcripts not covered)")
+      Log.debug("Chr #{ chr } failed (#{transcript_ranges.length} transcripts not covered): #{$!.message}")
+      Log.exception $!
       next
     end
 

data/share/install/STITCH/Rakefile

@@ -1,7 +1,7 @@
 require File.join(File.dirname(__FILE__),'../lib/rake_helper')
 
-define_source_tasks "protein_chemicals" => "http://stitch.embl.de/download/protein_chemical.links.v3.1.tsv.gz",
-  "chemicals" => "http://stitch.embl.de/download/chemicals.v3.1.tsv.gz"
+define_source_tasks "protein_chemicals" => "http://stitch.embl.de/download/protein_chemical.links.v4.0.tsv.gz",
+  "chemicals" => "http://stitch.embl.de/download/chemicals.v4.0.tsv.gz"
 
 process_tsv :protein_chemical, 'protein_chemicals',
   :key => 1,

data/share/install/STRING/Rakefile

@@ -1,6 +1,6 @@
 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"
+define_source_tasks "protein_protein" => "http://string-db.org/newstring_download/protein.links.v9.1.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']

data/test/rbbt/sources/test_biomart.rb

@@ -9,7 +9,7 @@ require 'test/unit'
 class TestBioMart < Test::Unit::TestCase
 
   def setup
-    BioMart.set_archive "jun2011"
+    BioMart.set_archive Organism.default_code("Hsa")
   end
 
   def teardown

data/test/rbbt/sources/test_organism.rb

@@ -54,7 +54,7 @@ class TestOrganism < Test::Unit::TestCase
   def test_lift_over
     mutation_19 = "19:21131664:T"
     mutation_18 = "19:20923504:T"
-    source_build = "Hsa/jun2011"
+    source_build = Organism.default_code("Hsa")
     target_build = "Hsa/may2009"
 
     assert_equal mutation_18, Organism.liftOver([mutation_19], source_build, target_build).first
@@ -63,7 +63,7 @@ class TestOrganism < Test::Unit::TestCase
 
   def _test_orhtolog
     require 'rbbt/entity/gene'
-    assert_equal ["ENSG00000133703"], Gene.setup("Kras", "Associated Gene Name", "Mmu/jun2011").ensembl.ortholog("Hsa/jun2011")
+    assert_equal ["ENSG00000133703"], Gene.setup("Kras", "Associated Gene Name", "Mmu/jun2011").ensembl.ortholog(Organism.default_code("Hsa"))
   end
 
   #def _test_genes_at_chromosome

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-sources
 version: !ruby/object:Gem::Version
-  version: 3.0.14
+  version: 3.0.16
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-08-15 00:00:00.000000000 Z
+date: 2014-08-26 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util