Module: Organism
- Extended by:
- Resource
- Defined in:
- lib/rbbt/sources/organism.rb
Defined Under Namespace
Classes: OrganismNotProcessedError
Constant Summary collapse
- ARCHIVE_MONTH_INDEX =
{}
Class Method Summary collapse
- .allowed_biomart_archives ⇒ Object
- .attach_translations(org, tsv, target = nil, fields = nil, options = {}) ⇒ Object
- .chromosome_sizes(organism = Organism.default_code("Hsa")) ⇒ Object
- .compare_archives(a1, a2) ⇒ Object
- .default_code(organism = "Hsa") ⇒ Object
- .entrez_taxid_organism(taxid) ⇒ Object
- .gene_list_bases(genes, organism = nil) ⇒ Object
- .gene_list_exon_bases(genes, organism = nil) ⇒ Object
- .GRC_build(organism) ⇒ Object
- .guess_id(org, values) ⇒ Object
- .hg_build(organism) ⇒ Object
- .installable_organisms ⇒ Object
- .installed_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
- .organism_codes(organism = nil) ⇒ Object
- .organism_for_build(build) ⇒ Object
- .organisms ⇒ Object
- .prepared_organisms ⇒ Object
- .scientific_name(organism) ⇒ Object
Class Method Details
.allowed_biomart_archives ⇒ Object
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# File 'lib/rbbt/sources/organism.rb', line 59 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 185 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 |
.chromosome_sizes(organism = Organism.default_code("Hsa")) ⇒ Object
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# File 'lib/rbbt/sources/organism.rb', line 320 def self.chromosome_sizes(organism = Organism.default_code("Hsa")) chromosome_sizes = {} Organism[organism].glob_all("chromosome_*").each do |file| chromosome = file.split("_").last.split(".").first size = if Open.gzip?(file) || Open.bgzip?(file) CMD.cmd("zcat '#{ file }' | wc -c ").read else File.size(file) end chromosome_sizes[chromosome] = size.to_i end chromosome_sizes end |
.compare_archives(a1, a2) ⇒ Object
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# File 'lib/rbbt/sources/organism.rb', line 12 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 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 y1 = y1.to_f y2 = y2.to_f ycmp = y1 <=> y2 return ycmp unless ycmp == 0 ARCHIVE_MONTH_INDEX[m1] <=> ARCHIVE_MONTH_INDEX[m2] end |
.default_code(organism = "Hsa") ⇒ Object
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# File 'lib/rbbt/sources/organism.rb', line 31 def self.default_code(organism = "Hsa") organism.split("/").first << "/feb2014" end |
.entrez_taxid_organism(taxid) ⇒ Object
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# File 'lib/rbbt/sources/organism.rb', line 260 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 |
.gene_list_bases(genes, organism = nil) ⇒ Object
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# File 'lib/rbbt/sources/organism.rb', line 270 def self.gene_list_bases(genes, organism = nil) if genes.respond_to? :orgnanism organism = genes.organism if organism.nil? genes = genes.clean_annotations end organism ||= "Hsa" @@gene_start_end ||= {} gene_start_end = @@gene_start_end[organism] ||= Organism.gene_positions(organism).tsv(:persist => true, :key_field => "Ensembl Gene ID", :fields => ["Gene Start", "Gene End"], :type => :list, :cast => :to_i, :unmamed => true) ranges = genes.collect{|gene| start, eend = gene_start_end[gene] if start.nil? or eend.nil? Log.low "Gene #{ gene } does not have range" next end (start..eend) }.compact Misc.total_length(ranges) end |
.gene_list_exon_bases(genes, organism = nil) ⇒ Object
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# File 'lib/rbbt/sources/organism.rb', line 292 def self.gene_list_exon_bases(genes, organism = nil) if genes.respond_to? :orgnanism organism = genes.organism if organism.nil? genes = genes.clean_annotations end organism ||= "Hsa" @@gene_exons_tsv ||= {} gene_exons = @@gene_exons_tsv[organism] ||= Organism.exons(organism).tsv(:persist => true, :key_field => "Ensembl Gene ID", :fields => ["Ensembl Exon ID"], :type => :flat, :merge => true, :unnamed => true) @@exon_range_tsv ||= {} exon_ranges = @@exon_range_tsv[organism] ||= Organism.exons(organism).tsv(:persist => true, :fields => ["Exon Chr Start", "Exon Chr End"], :type => :list, :cast => :to_i, :unnamed => true) exons = gene_exons.values_at(*genes).compact.flatten.uniq exon_ranges = exons.collect{|exon| if not exon_ranges.include? exon Log.low "Exon #{ exon } does not have range" next end pos = exon_ranges[exon] (pos.first..pos.last) }.compact Misc.total_length(exon_ranges) end |
.GRC_build(organism) ⇒ Object
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# File 'lib/rbbt/sources/organism.rb', line 104 def self.GRC_build(organism) require 'rbbt/sources/ensembl_ftp' return organism if organism =~ /^hg\d\d$/ return 'hg19' unless organism =~ /\// species, date = organism.split("/") case species when "Hsa" date = organism.split("/")[1] release = Ensembl.releases[date] release_number = release.sub(/.*-/,'').to_i if release_number <= 54 'GRCh36' elsif release_number <= 75 'GRCh37' else 'GRCh38' end when "Mmu" "GRCm38" when "Rno" "Rnor_6.0" else raise "Only organism 'Hsa' (Homo sapiens) and Mmu (Mus musculus) supported" end end |
.guess_id(org, values) ⇒ Object
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# File 'lib/rbbt/sources/organism.rb', line 223 def self.guess_id(org, values) field_matches = TSV.field_match_counts(Organism.identifiers(org).produce, values) best = nil best_count = 0 field_matches.each do |field,count| if count > best_count best = field best_count = count end end [best, best_count] end |
.hg_build(organism) ⇒ Object
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# File 'lib/rbbt/sources/organism.rb', line 73 def self.hg_build(organism) require 'rbbt/sources/ensembl_ftp' return organism if organism =~ /^hg\d\d$/ return 'hg19' unless organism =~ /\// species, date = organism.split("/") case species when "Hsa" date = organism.split("/")[1] release = Ensembl.releases[date] release_number = release.sub(/.*-/,'').to_i if release_number <= 54 'hg18' elsif release_number <= 75 'hg19' else 'hg38' end when "Mmu" "mm10" when "Rno" "rn6" else raise "Only organism 'Hsa' (Homo sapiens), 'Rno' (Rattus norvegicus), and Mmu (Mus musculus) supported" end end |
.installable_organisms ⇒ Object
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# File 'lib/rbbt/sources/organism.rb', line 55 def self.installable_organisms self.installed_organisms end |
.installed_organisms ⇒ Object
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# File 'lib/rbbt/sources/organism.rb', line 45 def self.installed_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 256 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 143 def self.liftOver(positions, source, target) source_hg = hg_build(source) target_hg = hg_build(target) map_url = "http://hgdownload.cse.ucsc.edu/goldenPath/#{source_hg}/liftOver/#{source_hg}To#{target_hg.sub('h', 'H')}.over.chain.gz" 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 197 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 244 def self.organism(name) installable_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 250 def self.organism_code(name) organisms.select{|organism| organism == name or Organism.scientific_name(organism) =~ /#{ name }/i }.first end |
.organism_codes(organism = nil) ⇒ Object
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# File 'lib/rbbt/sources/organism.rb', line 35 def self.organism_codes(organism = nil) if organism Rbbt.etc.allowed_biomart_archives.list.collect{|build| [organism, build] * "/" } else Rbbt.etc.organisms.list.collect{|organism| organism =~ /\// ? organism : Rbbt.etc.allowed_biomart_archives.list.collect{|build| [organism, build] * "/" } + [organism] }.flatten.compact.uniq end end |
.organism_for_build(build) ⇒ Object
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# File 'lib/rbbt/sources/organism.rb', line 135 def self.organism_for_build(build) build = build.sub('_noalt', '') build_organism = Rbbt.etc.build_organism.tsv :type => :single build_organism[build] end |
.organisms ⇒ Object
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# File 'lib/rbbt/sources/organism.rb', line 236 def self.organisms Dir.glob(File.join(Organism.root.find, '*')).collect{|f| File.basename(f)} end |
.prepared_organisms ⇒ Object
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# File 'lib/rbbt/sources/organism.rb', line 49 def self.prepared_organisms Rbbt.share.organisms.glob_all("???/???????/{identifiers,chromosome_1,scientific_name}").collect{|f| [File.basename(File.dirname(File.dirname(f))), File.basename(File.dirname(f))] * "/" }.uniq end |
.scientific_name(organism) ⇒ Object
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# File 'lib/rbbt/sources/organism.rb', line 240 def self.scientific_name(organism) Organism[organism]["scientific_name"].produce.read.strip end |