Module: Organism
- Extended by:
- Resource
- Defined in:
- lib/rbbt/sources/organism.rb
Defined Under Namespace
Classes: OrganismNotProcessedError
Class Method Summary collapse
- .allowed_biomart_archives ⇒ Object
- .attach_translations(org, tsv, target = nil, fields = nil, options = {}) ⇒ Object
- .entrez_taxid_organism(taxid) ⇒ Object
- .guess_id(org, values) ⇒ Object
- .hg_build(organism) ⇒ Object
- .installable_organisms ⇒ Object
- .known_ids(name) ⇒ Object
- .liftOver(positions, source, target) ⇒ Object
- .normalize(org, list, target = nil, fields = nil, options = {}) ⇒ Object
- .organism(name) ⇒ Object
- .organism_code(name) ⇒ Object
- .organisms ⇒ Object
- .scientific_name(organism) ⇒ Object
Class Method Details
.allowed_biomart_archives ⇒ Object
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# File 'lib/rbbt/sources/organism.rb', line 13 def self.allowed_biomart_archives Rbbt.etc.allowed_biomart_archives.exists? ? Rbbt.etc.allowed_biomart_archives.list : nil end |
.attach_translations(org, tsv, target = nil, fields = nil, options = {}) ⇒ Object
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# File 'lib/rbbt/sources/organism.rb', line 90 def self.attach_translations(org, tsv, target = nil, fields = nil, = {}) Log.high "Attaching Translations for #{ org.inspect }, target #{target.inspect}, fields #{fields.inspect}" = Misc.add_defaults , :persist => true, :case_insensitive => false .merge! :key_field => target unless target.nil? .merge! :fields => fields unless fields.nil? index = identifiers(org).tsv tsv.attach index, :fields => [:key], :persist_input => true end |
.entrez_taxid_organism(taxid) ⇒ Object
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# File 'lib/rbbt/sources/organism.rb', line 157 def self.entrez_taxid_organism(taxid) all_organisms = Organism.installable_organisms all_organisms.each do |organism| return organism if Organism.entrez_taxids(organism).read.split("\n").include? taxid.to_s end raise "No organism identified for taxid #{taxid}. Supported organism are: #{all_organisms * ", "}" end |
.guess_id(org, values) ⇒ Object
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# File 'lib/rbbt/sources/organism.rb', line 128 def self.guess_id(org, values) field_matches = TSV.field_match_counts(Organism.identifiers(org).find, values) field_matches.sort_by{|field, count| count.to_i}.last end |
.hg_build(organism) ⇒ Object
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# File 'lib/rbbt/sources/organism.rb', line 28 def self.hg_build(organism) require 'rbbt/sources/ensembl_ftp' raise "Only organism 'Hsa' (Homo sapiens) supported" unless organism =~ /^Hsa/ return 'hg19' unless organism =~ /\// date = organism.split("/")[1] release = Ensembl.releases[date] release.sub(/.*-/,'').to_i > 54 ? 'hg19' : 'hg18' end |
.installable_organisms ⇒ Object
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# File 'lib/rbbt/sources/organism.rb', line 9 def self.installable_organisms Rbbt.share.install.Organism.find.glob('???').collect{|f| File.basename(f)} end |
.known_ids(name) ⇒ Object
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# File 'lib/rbbt/sources/organism.rb', line 153 def self.known_ids(name) TSV::Parser.new(Organism.identifiers(name).open).all_fields end |
.liftOver(positions, source, target) ⇒ Object
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# File 'lib/rbbt/sources/organism.rb', line 41 def self.liftOver(positions, source, target) source_hg = hg_build(source) target_hg = hg_build(target) case when (source_hg == 'hg19' and target_hg == 'hg18') map_url = "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg18.over.chain.gz" when (source_hg == 'hg18' and target_hg == 'hg19') map_url = "http://hgdownload.cse.ucsc.edu/goldenPath/hg18/liftOver/hg18ToHg19.over.chain.gz" else return positions end positions_bed = positions.collect{|position| chr, pos = position.split(":").values_at(0,1) ["chr" << chr, pos.to_i-1, pos, position] * "\t" } * "\n" + "\n" new_positions = {} TmpFile.with_file(positions_bed) do |source_bed| TmpFile.with_file() do |unmapped_file| TmpFile.with_file() do |map_file| Open.write(map_file, Open.read(map_url)) new_mutations = TmpFile.with_file() do |target_bed| FileUtils.chmod(755, Rbbt.software.opt.bin.liftOver.produce.find) CMD.cmd("#{Rbbt.software.opt.bin.liftOver.find} '#{source_bed}' '#{map_file}' '#{target_bed}' '#{unmapped_file}'").read Open.read(target_bed) do |line| chr, position_alt, position, name = line.chomp.split("\t") chr.sub! /chr/, '' old_chr, old_position, *rest = name.split(":") new_positions[name] = ([chr, position].concat rest) * ":" end end end end end positions.collect do |position| new_positions[position] end end |
.normalize(org, list, target = nil, fields = nil, options = {}) ⇒ Object
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# File 'lib/rbbt/sources/organism.rb', line 102 def self.normalize(org, list, target = nil, fields = nil, = {}) return [] if list.nil? or list.empty? = Misc.add_defaults , :persist => true, :case_insensitive => true, :double => false double = Misc. , :double .merge! :target => target unless target.nil? .merge! :fields => fields unless fields.nil? index = identifiers(org).index if Array === list if double index.values_at *list else index.values_at(*list).collect{|e| Misc.first e} end else if double index[list] else index[list].first end end end |
.organism(name) ⇒ Object
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# File 'lib/rbbt/sources/organism.rb', line 141 def self.organism(name) organisms.select{|organism| organism == name or Organism.scientific_name(organism) =~ /#{ name }/i }.first end |
.organism_code(name) ⇒ Object
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# File 'lib/rbbt/sources/organism.rb', line 147 def self.organism_code(name) organisms.select{|organism| organism == name or Organism.scientific_name(organism) =~ /#{ name }/i }.first end |
.organisms ⇒ Object
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# File 'lib/rbbt/sources/organism.rb', line 133 def self.organisms Dir.glob(File.join(Organism.root.find, '*')).collect{|f| File.basename(f)} end |
.scientific_name(organism) ⇒ Object
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# File 'lib/rbbt/sources/organism.rb', line 137 def self.scientific_name(organism) Organism[organism]["scientific_name"].produce.read.strip end |