Module: ID

Defined in:
lib/MARQ/ID.rb

Constant Summary collapse

DEFAULT_FORMAT_ALL =

DEFAULT_FORMAT_ALL = ‘Entrez Gene Id’

nil
DEFAULT_FORMATS = 
{}
@@supported = 
{}

Class Method Summary collapse

Class Method Details

.AILUN_translate(platform, genes) ⇒ Object 



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# File 'lib/MARQ/ID.rb', line 118

def self.AILUN_translate(platform, genes)
  index = Open.to_hash("ftp://ailun.stanford.edu/ailun/annotation/geo/#{platform}.annot.gz", :fix => proc{|l| l.match(/^(.*?)\t(.*?)\t.*/); $1.downcase + "\t" + $2 })
  index.values_at(*genes.collect{|code| code.strip.downcase}).collect{|v| v.nil? ? nil : v.first.first}
end

.DB_load(org, to = 0) ⇒ Object 



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# File 'lib/MARQ/ID.rb', line 16

def self.DB_load(org, to = 0)
  identifier_file = File.join(Rbbt.datadir,'organisms',org,'identifiers')
  tablename = "ID_#{org.to_s.strip}_#{to.to_s.strip}"
  
  if DBcache.has_table?(tablename)
    DBcache.drop(tablename)
  end

  DBcache.create(tablename, 'CHAR(50)', ['CHAR(50)'])

  require 'progress-monitor'

  total_fields = Organism.supported_ids(org).length
  
  Progress.monitor "Loading ID DB table for #{ org } - #{to}"
  total_fields.times{|field|
    Progress.monitor "Processing file. Field #{ field } / #{total_fields}"
    File.open(identifier_file).each{|l|
      next if l =~ /^#/
      codes = l.chomp.split(/\t/)

      native = codes[to]
      next if native.nil? || native == "" 

      other  = codes[field]
      next if other.nil? || other == ""
      

      #codes.collect{|c| c.split("|")}.flatten.compact.select{|c| c != ""}.uniq.each{|code|
      other.split("|").each{|code|
        begin
          DBcache.fast_add(tablename, code.downcase, [native])
        rescue
          puts $!.message
        end
      }
    }
  }
end

.id_position(org, id) ⇒ Object 



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# File 'lib/MARQ/ID.rb', line 10

def self.id_position(org, id)
  @@supported[org] ||= Organism.supported_ids(org)
  Organism.id_position(@@supported[org], id)
end

.translate_DB(org, genes, options = {}) ⇒ Object Also known as: translate 



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# File 'lib/MARQ/ID.rb', line 56

def self.translate_DB(org, genes, options = {})
  to = options[:to] || DEFAULT_FORMATS[org] || DEFAULT_FORMAT_ALL

  if to
    to = id_position(org, to)
  else 
    to = 0
  end

  tablename = "ID_#{org.to_s.strip}_#{to.to_s.strip}"
  DB_load(org, to) unless DBcache.has_table?(tablename)
  genes = genes.collect{|gene| gene.strip.downcase}
  DBcache.load(tablename, genes).values_at(*genes).collect{|gene| gene.first if gene}
end

.translate_grep(org, genes, options = {}) ⇒ Object 



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# File 'lib/MARQ/ID.rb', line 94

def self.translate_grep(org, genes, options = {})
  to = options[:to] || DEFAULT_FORMATS[org] || DEFAULT_FORMAT_ALL
  from = options[:from]

  options = {}
  options[:extra]  = [id_position(org, from)] if from
  options[:native] = id_position(org,to) if to
  options[:case_sensitive] ||= false

  genes = genes.collect{|gene| gene.strip if gene}
  genes = genes.collect{|gene| gene.downcase} unless options[:case_sensitive] 

  #genes_re = '\(^\|[' + "\t" + '|]\)' + genes.join('\|') + '\($\|[' + "\t" + '|]\)'
  #cmd = "cat #{File.join(Rbbt.datadir,'organisms',org,'identifiers')}|grep -i '#{genes_re}'"
  genes_re = '(?:^|[\t\|])(?:' + genes.join('|') + ')(?:$|[\t\|])'
  cmd = "cat #{File.join(Rbbt.datadir,'organisms',org,'identifiers')}|ruby -lne 'puts $_ if $_ =~ /#{genes_re}/i'"

  index = Index.index(IO::popen(cmd), options)

  index.values_at(*genes)

end

.translate_index(org, genes, options = {}) ⇒ Object 



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# File 'lib/MARQ/ID.rb', line 71

def self.translate_index(org, genes, options = {})
  genes = genes.collect{|gene| gene.strip if gene}
  to = options[:to] || DEFAULT_FORMATS[org] || DEFAULT_FORMAT_ALL
  from = options[:from]
  @indexes ||= {}
  if  @indexes[org.to_s + to.to_s + from.to_s].nil?
    puts "Loading #{ org }"
    options = {}
    options[:other] = [from] if from
    options[:native] = to if to
    options[:case_sensitive] = false
    
    @indexes[org.to_s + to.to_s + from.to_s] = Organism.id_index(org, options)
  end

  index =  @indexes[org.to_s + to.to_s + from.to_s]
  
  return genes.collect{|code| 
    code.nil? || code == "" ? nil : index[code]
  }
end