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

Class Method Details

.allowed_biomart_archives ⇒ Object 



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# File 'lib/rbbt/sources/organism.rb', line 65

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 191

def self.attach_translations(org, tsv, target = nil, fields = nil, options = {})
  Log.high "Attaching Translations for #{ org.inspect }, target #{target.inspect}, fields #{fields.inspect}"
  options = Misc.add_defaults options, :persist => true, :case_insensitive => false

  options.merge! :key_field    => target unless target.nil?
  options.merge! :fields => fields unless fields.nil?

  index = identifiers(org).tsv options

  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 335

def self.chromosome_sizes(organism = Organism.default_code("Hsa"))
  chromosome_sizes = {}

  Organism.chromosomes(organism).produce.tsv.each do |chr|
    file = Organism[organism]["chromosome_#{chr}"].produce.find
    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 16

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 35

def self.default_code(organism = "Hsa")
  latest = Rbbt.etc.allowed_biomart_archives.list.sort{|a,b| compare_archives(a, b)}.last
  organism.split("/").first << "/" << latest
end

.entrez_taxid_organism(taxid) ⇒ Object 



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# File 'lib/rbbt/sources/organism.rb', line 275

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 285

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, :unnamed => 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 307

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, with_release = false) ⇒ Object 



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# File 'lib/rbbt/sources/organism.rb', line 103

def self.GRC_build(organism, with_release = false)
  require 'rbbt/sources/ensembl_ftp'
  return organism if organism =~ /^GRC$/

  if organism == "hg19" || organism == "b37"
    return "GRCh37"
  elsif organism == "hg38"
    return "GRCh38"
  end

  return self.GRC_build(default_code(organism)) unless organism =~ /\//

  species, date = organism.split("/")

  build = 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

  (release_number && with_release) ? build + "." + release_number.to_s : build
end

.guess_id(org, values) ⇒ Object 



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# File 'lib/rbbt/sources/organism.rb', line 229

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 71

def self.hg_build(organism)
  require 'rbbt/sources/ensembl_ftp'
  organism = organism.strip 
  return organism if organism =~ /^hg\d\d$/

  return organism 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 61

def self.installable_organisms
  self.installed_organisms
end

.installed_organisms ⇒ Object 



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# File 'lib/rbbt/sources/organism.rb', line 50

def self.installed_organisms
  Rbbt.share.install.Organism.find.glob('???').collect{|f| File.basename(f) } + 
  Rbbt.share.install.Organism.find.glob('*.rake').collect{|f| File.basename(f).sub(/\.rake/, '') }
end

.known_ids(name) ⇒ Object 



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# File 'lib/rbbt/sources/organism.rb', line 271

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 150

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|
          CMD.cmd_log(:liftOver, "'#{source_bed}' '#{map_file}' '#{target_bed}' '#{unmapped_file}'")
          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

.make_organism(name, long = false) ⇒ Object 



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# File 'lib/rbbt/sources/organism.rb', line 250

def self.make_organism(name, long = false)
  first, _, second = name.partition(/[ _]/)
  if long
    first[0].upcase + second.downcase.gsub(/[^a-z]/,'')
  else
    first[0].upcase + second[0..1].downcase
  end
end

.normalize(org, list, target = nil, fields = nil, options = {}) ⇒ Object 



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# File 'lib/rbbt/sources/organism.rb', line 203

def self.normalize(org, list, target = nil, fields = nil, options = {})
  return [] if list.nil? or list.empty?
  options = Misc.add_defaults options, :persist => true, :case_insensitive => true, :double => false
  double = Misc.process_options options, :double


  options.merge! :target => target unless target.nil?
  options.merge! :fields => fields unless fields.nil?

  index = identifiers(org).index options

  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 259

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 265

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 40

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 142

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 242

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 55

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

.rake_organism_helper ⇒ Object 



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# File 'lib/rbbt/sources/organism.rb', line 12

def self.rake_organism_helper
  Rbbt.share.install.Organism["organism_helpers.rb"].find
end

.scientific_name(organism) ⇒ Object 



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# File 'lib/rbbt/sources/organism.rb', line 246

def self.scientific_name(organism)
  Organism[organism].scientific_name.read.strip
end