rbbt-sources 3.0.19 → 3.0.20

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 09103120ab258ebec5b5229f3af3b8f81b08a09d
-  data.tar.gz: 859133185352820244010f79dcbff16fb74c8472
+  metadata.gz: d10e3a8a64d8a1c63059a3d798f4043381a7a729
+  data.tar.gz: 36b6a7794b2c29ff6fc7b29e3d3e6c23370f93e3
 SHA512:
-  metadata.gz: 973ad5daac0276bf77ca2d8379415ffb8933dbee131a40795c07316b4f78af6e1776a24c4036b52248f435864264a339d7f3205516094f2d332e5e8a2032f59e
-  data.tar.gz: 2ff6ccd29f102f4c256a4aa84e151210e6fb51586dc97e1f19ed08b9ab7b0e9afcbc61ed39543b9d0a1be68edcce2627ab92ebc4afc1537f124a6cd4f7306499
+  metadata.gz: 5c64b9b8f739a3c1ee5c48ac1d2cb8a17307d2d1831f135133c34406eff1487a973af8c90ee5de504c45481002ec1fa403ee83ac80f1a89c49d6afbe9dbcc0ca
+  data.tar.gz: 30e958a1aafabb3e4329341b8b0d268cc2b68799ca9049a7d56779e424fe40f0f85c670811ac6c58e398575a5ea6c08140d2d6079f5324561f06a802de27ea8e

data/lib/rbbt/sources/biomart.rb

@@ -56,7 +56,7 @@ module BioMart
   end
 
   def self.get(database, main, attrs = nil, filters = nil, data = nil, open_options = {})
-    open_options = Misc.add_defaults :wget_options => {"--read-timeout=" => 9000, "--tries=" => 1}
+    open_options = Misc.add_defaults open_options, :wget_options => {"--read-timeout=" => 9000, "--tries=" => 1}
     repeats = true
     attrs   ||= []
     filters ||= ["with_#{main}"]
@@ -82,6 +82,7 @@ module BioMart
     url = Thread.current['archive_url'] ? Thread.current['archive_url'] + query.gsub(/\n/,' ') : BIOMART_URL + query.gsub(/\n/,' ')
 
     begin
+      iii open_options
       response = Open.read(url, open_options.dup)
     rescue
       Open.remove_from_cache url, open_options
@@ -137,7 +138,6 @@ module BioMart
     open_options = Misc.add_defaults open_options, :nocache => false, :filename => nil, :field_names => nil, :by_chr => false
     filename, field_names, by_chr = Misc.process_options open_options, :filename, :field_names, :by_chr
     attrs   ||= []
-
     open_options = Misc.add_defaults open_options, :keep_empty => false, :merge => true
 
     Log.low "BioMart query: '#{main}' [#{(attrs || []) * ', '}] [#{(filters || []) * ', '}] #{open_options.inspect}"
@@ -161,10 +161,10 @@ module BioMart
     if chunks.any?
       chunks.each_with_index{|chunk,i|
         Log.low "Chunk #{ i + 1 } / #{chunks.length}: [#{chunk * ", "}]"
-        data = get(database, main, chunk, filters, data, open_options)
+        data = get(database, main, chunk, filters, data, open_options.dup)
       }
     else
-      data = get(database, main, [], filters, data, open_options)
+      data = get(database, main, [], filters, data, open_options.dup)
     end
 
     open_options[:filename] = "BioMart[#{main}+#{attrs.length}]"

data/lib/rbbt/sources/organism.rb

@@ -228,3 +228,4 @@ module Organism
     Misc.total_length(exon_ranges)
   end
 end
+

data/lib/rbbt/sources/pfam.rb

@@ -76,6 +76,7 @@ if defined? Entity
 
 
   module InterProDomain
+    extend Entity
     property :pfam => :array2single do
       InterPro.pfam_index.values_at(*self).
         each{|domain| domain.organism = organism if domain.respond_to? :organism }

data/share/install/NCI/Rakefile

@@ -6,6 +6,8 @@ module NCI
     doc = Nokogiri::XML(xml)
     pathways = {}
 
+    #{{{ Molecules
+    
     molecules = {}
     doc.xpath("//Molecule").each do |molecule|
       id = molecule.attribute('id').value
@@ -15,6 +17,8 @@ module NCI
     end
 
 
+    #{{{ Interactions
+
     interactions = {}
     doc.xpath("//Interaction").each do |interaction|
       id = interaction.attribute('id').value
@@ -25,6 +29,8 @@ module NCI
       interactions[id] = {:xml => interaction, :molecule_ids => molecule_ids, :pathway_ids => pathway_ids}
     end
 
+    #{{{ Pathways
+
     doc.xpath("//Pathway").each do |pathway|
       id = pathway.attribute('id').value
       subnet = pathway.attribute('subnet').value
@@ -32,8 +38,8 @@ module NCI
       short_name = pathway.xpath('ShortName').first.content if get_short_name
 
       interaction_ids = pathway.xpath("PathwayComponentList/PathwayComponent").collect{|component| component.attribute("interaction_idref").value}
-
       pathway_interactions = interaction_ids.collect{|i| interactions[i]}
+
       pathway_molecule_ids = pathway_interactions.collect{|info| info[:molecule_ids]}.compact.flatten
 
       pathway_uniprot_ids = pathway_molecule_ids.collect do |i| 
@@ -47,20 +53,22 @@ module NCI
       end
     end
     
+    #{{{ Sub-pathways ???
+    
     doc.xpath("//Pathway").each do |pathway|
       id = pathway.attribute('id').value
       subnet = pathway.attribute('subnet').value
       name = pathway.xpath('LongName').first.content
 
       interaction_ids = pathway.xpath("PathwayComponentList/PathwayComponent").collect{|component| component.attribute("interaction_idref").value}
-
       pathway_interactions = interaction_ids.collect{|i| interactions[i]}
+
       pathway_subnet_ids = pathway_interactions.collect{|info| info[:pathway_ids]}.compact.flatten
 
       pathway_subnet_ids.collect do |nid| 
         next unless pathways.include? nid
-        new_genes = pathways[id].last
-        pathways[nid][1] = (pathways[nid][1] + new_genes).uniq
+        new_genes = pathways[nid].last
+        pathways[id][1] = (pathways[id][1] + new_genes).uniq
       end
     end
 

data/share/install/Organism/organism_helpers.rb

@@ -353,6 +353,7 @@ file 'exon_offsets' => %w(exons transcript_exons gene_transcripts transcripts tr
 end
 
 file 'gene_go' do |t|
+  iii 1
   if File.basename(FileUtils.pwd) =~ /^[a-z]{3}([0-9]{4})$/i and $1.to_i <= 2009
     goterms = BioMart.tsv($biomart_db, $biomart_ensembl_gene, $biomart_go_2009, [], nil, :type => :double, :namespace => Thread.current['namespace'])
 

data/test/rbbt/sources/test_biomart.rb

@@ -70,5 +70,3 @@ class TestBioMart < Test::Unit::TestCase
     end
   end
 end
-
-

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-sources
 version: !ruby/object:Gem::Version
-  version: 3.0.19
+  version: 3.0.20
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-10-17 00:00:00.000000000 Z
+date: 2015-01-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util