rbbt-sources 3.0.19 → 3.0.20

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checksums.yaml CHANGED
@@ -1,7 +1,7 @@
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  SHA1:
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+ data.tar.gz: 36b6a7794b2c29ff6fc7b29e3d3e6c23370f93e3
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  SHA512:
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@@ -56,7 +56,7 @@ module BioMart
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  end
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  def self.get(database, main, attrs = nil, filters = nil, data = nil, open_options = {})
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- open_options = Misc.add_defaults :wget_options => {"--read-timeout=" => 9000, "--tries=" => 1}
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+ open_options = Misc.add_defaults open_options, :wget_options => {"--read-timeout=" => 9000, "--tries=" => 1}
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  repeats = true
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  attrs ||= []
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  filters ||= ["with_#{main}"]
@@ -82,6 +82,7 @@ module BioMart
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  url = Thread.current['archive_url'] ? Thread.current['archive_url'] + query.gsub(/\n/,' ') : BIOMART_URL + query.gsub(/\n/,' ')
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  begin
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+ iii open_options
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  response = Open.read(url, open_options.dup)
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  rescue
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  Open.remove_from_cache url, open_options
@@ -137,7 +138,6 @@ module BioMart
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  open_options = Misc.add_defaults open_options, :nocache => false, :filename => nil, :field_names => nil, :by_chr => false
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  filename, field_names, by_chr = Misc.process_options open_options, :filename, :field_names, :by_chr
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  attrs ||= []
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-
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  open_options = Misc.add_defaults open_options, :keep_empty => false, :merge => true
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  Log.low "BioMart query: '#{main}' [#{(attrs || []) * ', '}] [#{(filters || []) * ', '}] #{open_options.inspect}"
@@ -161,10 +161,10 @@ module BioMart
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  if chunks.any?
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  chunks.each_with_index{|chunk,i|
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  Log.low "Chunk #{ i + 1 } / #{chunks.length}: [#{chunk * ", "}]"
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- data = get(database, main, chunk, filters, data, open_options)
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+ data = get(database, main, chunk, filters, data, open_options.dup)
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  }
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  else
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- data = get(database, main, [], filters, data, open_options)
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+ data = get(database, main, [], filters, data, open_options.dup)
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  end
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  open_options[:filename] = "BioMart[#{main}+#{attrs.length}]"
@@ -228,3 +228,4 @@ module Organism
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  Misc.total_length(exon_ranges)
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  end
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  end
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+
@@ -76,6 +76,7 @@ if defined? Entity
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  module InterProDomain
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+ extend Entity
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  property :pfam => :array2single do
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  InterPro.pfam_index.values_at(*self).
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  each{|domain| domain.organism = organism if domain.respond_to? :organism }
@@ -6,6 +6,8 @@ module NCI
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  doc = Nokogiri::XML(xml)
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  pathways = {}
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+ #{{{ Molecules
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+
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  molecules = {}
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  doc.xpath("//Molecule").each do |molecule|
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  id = molecule.attribute('id').value
@@ -15,6 +17,8 @@ module NCI
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  end
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+ #{{{ Interactions
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+
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  interactions = {}
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  doc.xpath("//Interaction").each do |interaction|
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  id = interaction.attribute('id').value
@@ -25,6 +29,8 @@ module NCI
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  interactions[id] = {:xml => interaction, :molecule_ids => molecule_ids, :pathway_ids => pathway_ids}
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  end
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+ #{{{ Pathways
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+
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  doc.xpath("//Pathway").each do |pathway|
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  id = pathway.attribute('id').value
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  subnet = pathway.attribute('subnet').value
@@ -32,8 +38,8 @@ module NCI
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  short_name = pathway.xpath('ShortName').first.content if get_short_name
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  interaction_ids = pathway.xpath("PathwayComponentList/PathwayComponent").collect{|component| component.attribute("interaction_idref").value}
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-
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  pathway_interactions = interaction_ids.collect{|i| interactions[i]}
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+
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  pathway_molecule_ids = pathway_interactions.collect{|info| info[:molecule_ids]}.compact.flatten
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  pathway_uniprot_ids = pathway_molecule_ids.collect do |i|
@@ -47,20 +53,22 @@ module NCI
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  end
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  end
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+ #{{{ Sub-pathways ???
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+
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  doc.xpath("//Pathway").each do |pathway|
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  id = pathway.attribute('id').value
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  subnet = pathway.attribute('subnet').value
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  name = pathway.xpath('LongName').first.content
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  interaction_ids = pathway.xpath("PathwayComponentList/PathwayComponent").collect{|component| component.attribute("interaction_idref").value}
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-
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  pathway_interactions = interaction_ids.collect{|i| interactions[i]}
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+
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  pathway_subnet_ids = pathway_interactions.collect{|info| info[:pathway_ids]}.compact.flatten
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  pathway_subnet_ids.collect do |nid|
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  next unless pathways.include? nid
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- new_genes = pathways[id].last
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- pathways[nid][1] = (pathways[nid][1] + new_genes).uniq
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+ new_genes = pathways[nid].last
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+ pathways[id][1] = (pathways[id][1] + new_genes).uniq
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  end
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  end
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@@ -353,6 +353,7 @@ file 'exon_offsets' => %w(exons transcript_exons gene_transcripts transcripts tr
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  end
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  file 'gene_go' do |t|
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+ iii 1
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  if File.basename(FileUtils.pwd) =~ /^[a-z]{3}([0-9]{4})$/i and $1.to_i <= 2009
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  goterms = BioMart.tsv($biomart_db, $biomart_ensembl_gene, $biomart_go_2009, [], nil, :type => :double, :namespace => Thread.current['namespace'])
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@@ -70,5 +70,3 @@ class TestBioMart < Test::Unit::TestCase
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  end
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  end
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  end
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-
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-
metadata CHANGED
@@ -1,14 +1,14 @@
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  --- !ruby/object:Gem::Specification
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  name: rbbt-sources
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  version: !ruby/object:Gem::Version
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- version: 3.0.19
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+ version: 3.0.20
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  platform: ruby
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  authors:
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  - Miguel Vazquez
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2014-10-17 00:00:00.000000000 Z
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+ date: 2015-01-14 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: rbbt-util