rbbt-sources 3.0.34 → 3.0.35

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 70e1df68dd361e27ccf4fa97f3d1566843aa9782
-  data.tar.gz: 700991e8dbbd83e10c956960d530692da3feff7a
+  metadata.gz: 083db9d4de7fef1d0b47db55ebb186dd64f1415e
+  data.tar.gz: b54b80b4efa6d2b58a67b2545b3f7747c11b224f
 SHA512:
-  metadata.gz: 2f3eae3226db83878bb5fd5b58f7562ab38f3a7f36fbc4dc94752e4df0793834d9d2f451dcd0557275332e7ae81c2ec6ef10fde1f139f4eae089b8887bcb998d
-  data.tar.gz: 0c3e5d7294eaf73ce9c192dfa3073921ab5961936f87eb1578dc38b94b43147d559475f019a3c9294314fa603bd754dcba82db4040cd1f46180f0b5edf648df6
+  metadata.gz: 3e88c53567e931644df016f4fed03154cb057ecc422df4f0105c4748a36e91e9c46798ceab150511abb43d8df6a12ff36fa6de5f199070bd435d8ce1df6d7279
+  data.tar.gz: 2323da3182c3c50048dbb471f3bec1e3d3ebf2860de22dda0a1fc13088a52e8f22e89174b96c3a88a89aa9653990bdbd533931bb3e0b834031eabe5eadfa1ce5

data/lib/rbbt/sources/biomart.rb

@@ -190,27 +190,27 @@ module BioMart
   def self.tsv(database, main, attrs = nil, filters = nil, data = nil, open_options = {})
     attrs ||= []
 
-    if current_archive = Thread.current['archive'] 
-      missing = MISSING_IN_ARCHIVE['all'] || []
-      missing += MISSING_IN_ARCHIVE[current_archive] || []
-      MISSING_IN_ARCHIVE.each do |k,v|
-        if k =~ /^<(.*)/ 
-          t = $1.strip
-          missing+=v if Organism.compare_archives(current_archive, t) == -1
-        elsif k=~ /^>(.*)/ 
-          t = $1.strip
-          missing+=v if Organism.compare_archives(current_archive, t) == 1
-        end
-      end
-      attrs = attrs.uniq.reject{|attr| missing.include? attr[1]}
-      changes = {}
-      missing.select{|m| m.include? "~" }.each do |str|
-        orig,_sep, new = str.partition "~"
-        changes[orig] = new
+    current_archive = Thread.current['archive'] 
+    missing = MISSING_IN_ARCHIVE['all'] || []
+    missing += MISSING_IN_ARCHIVE[current_archive] || [] if current_archive
+
+    MISSING_IN_ARCHIVE.each do |k,v|
+      if k =~ /^<(.*)/ 
+        t = $1.strip
+        missing+=v if Organism.compare_archives(current_archive, t) == -1
+      elsif k=~ /^>(.*)/ 
+        t = $1.strip
+        missing+=v if Organism.compare_archives(current_archive, t) == 1
       end
-      attrs = attrs.collect{|n,k| [n, changes[k] || k] }
-      attrs
     end
+    attrs = attrs.uniq.reject{|attr| missing.include? attr[1]}
+    changes = {}
+    missing.select{|m| m.include? "~" }.each do |str|
+      orig,_sep, new = str.partition "~"
+      changes[orig] = new
+    end
+    attrs = attrs.collect{|n,k| [n, changes[k] || k] }
+    attrs
 
 
     codes = attrs.collect{|attr| attr[1]}

data/lib/rbbt/sources/organism.rb

@@ -9,9 +9,11 @@ module Organism
   ARCHIVE_MONTH_INDEX = {}
   %w(jan feb mar apr may jun jul aug sep oct nov dec).each_with_index{|d,i| ARCHIVE_MONTH_INDEX[d] = i }
   def self.compare_archives(a1, a2)
+    a1 = a1.partition("/").last if a1 and a1.include? "/"
+    a2 = a2.partition("/").last if a2 and a2.include? "/"
     return 0 if a1 == a2
-    return -1 if a1 =~ /\// and not a2 =~ /\//
-    return 1 if a2 =~ /\// and not a1 =~ /\//
+    return -1 if a1 and a2.nil?
+    return 1 if a1.nil? and a2
 
     m1,y1 = a1.match(/(...)(\d+)/).values_at 1, 2
     m2,y2 = a2.match(/(...)(\d+)/).values_at 1, 2

data/test/rbbt/sources/test_organism.rb

@@ -5,37 +5,37 @@ require 'rbbt/sources/ensembl_ftp'
 
 class TestOrganism < Test::Unit::TestCase
 
-  def _test_known_ids
+  def test_known_ids
     assert Organism.known_ids("Hsa").include?("Associated Gene Name")
   end
 
-  def _test_location
+  def test_location
     assert_equal "share/organisms/Sce/identifiers", Organism.identifiers('Sce')
   end
 
-  def _test_identifiers
+  def test_identifiers
     assert Organism.identifiers('Hsa').tsv(:key_field => "Entrez Gene ID", :persist => true)['1020']["Associated Gene Name"].include?('CDK5')
     assert Organism.identifiers('Sce').tsv(:persist => true)['S000006120']["Ensembl Gene ID"].include?('YPL199C')
     assert Organism.identifiers("Sce").tsv(:persist => true)['S000006120']["Ensembl Gene ID"].include?('YPL199C')
   end
 
-  def _test_lexicon
+  def test_lexicon
     assert TSV.open(Organism.lexicon('Sce'))['S000006120'].flatten.include?('YPL199C')
   end
 
-  def _test_guess_id
+  def test_guess_id
     ensembl = %w(YOL044W YDR289C YAL034C YGR246C ARS519 tH(GUG)E2 YDR218C YLR002C YGL224C)
     gene_name = %w(SNR64 MIP1 MRPS18 TFB2 JEN1 IVY1 TRS33 GAS3)
     assert_equal "Associated Gene Name", Organism.guess_id("Sce", gene_name).first
     assert_equal "Ensembl Gene ID", Organism.guess_id("Sce", ensembl).first
   end
 
-  def _test_organisms
+  def test_organisms
     assert Organism.organisms.include? "Hsa"
     assert_equal "Hsa", Organism.organism("Homo sapiens")
   end
 
-  def _test_attach_translations
+  def test_attach_translations
     tsv = TSV.setup({"1020" => []}, :type => :list)
     tsv.key_field = "Entrez Gene ID"
     tsv.fields = []
@@ -47,7 +47,7 @@ class TestOrganism < Test::Unit::TestCase
     assert_equal "CDK5", tsv["1020"]["Associated Gene Name"]
   end
 
-  def _test_entrez_taxids
+  def test_entrez_taxids
     assert_equal "Hsa", Organism.entrez_taxid_organism('9606')
   end
 
@@ -61,22 +61,22 @@ class TestOrganism < Test::Unit::TestCase
     assert_equal mutation_19, Organism.liftOver([mutation_18], target_build, source_build).first
   end
 
-  def _test_orhtolog
+  def test_orhtolog
     require 'rbbt/entity/gene'
     assert_equal ["ENSG00000133703"], Gene.setup("Kras", "Associated Gene Name", "Mmu/jun2011").ensembl.ortholog(Organism.default_code("Hsa"))
   end
 
-  #def _test_genes_at_chromosome
+  #def test_genes_at_chromosome
   #  pos = [12, 117799500]
   #  assert_equal "ENSG00000089250", Organism::Hsa.genes_at_chromosome_positions(pos.first, pos.last)
   #end
 
-  #def _test_genes_at_chromosome_array
+  #def test_genes_at_chromosome_array
   #  pos = [12, [117799500, 106903900]]
   #  assert_equal ["ENSG00000089250", "ENSG00000013503"], Organism::Hsa.genes_at_chromosome_positions(pos.first, pos.last)
   #end
  
-  #def _test_genes_at_genomic_positions
+  #def test_genes_at_genomic_positions
   #  pos = [[12, 117799500], [12, 106903900], [1, 115259500]]
   #  assert_equal ["ENSG00000089250", "ENSG00000013503", "ENSG00000213281"], Organism::Hsa.genes_at_genomic_positions(pos)
   #end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-sources
 version: !ruby/object:Gem::Version
-  version: 3.0.34
+  version: 3.0.35
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-10-09 00:00:00.000000000 Z
+date: 2015-11-06 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util