Top Level Namespace

Includes:
Ensembl::Core, Ensembl::Variation

Defined Under Namespace

Modules: Ensembl, IRB

Instance Method Summary collapse

Methods included from Ensembl::Core

#canonical_transcript

Instance Method Details

#get_consequence(chr, start, stop, alleles, strand, name) ⇒ Object 



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# File 'bin/variation_effect_predictor', line 76

def get_consequence(chr,start,stop,alleles,strand,name)
  variation = VariationFeature.new(:seq_region_id => SeqRegion.find_by_name(chr).seq_region_id,
                                   :seq_region_start => start, 
                                   :seq_region_end => stop, 
                                   :allele_string => alleles, 
                                   :seq_region_strand => strand, 
                                   :variation_name => name
                                   )
  return variation.transcript_variations
end

#run_calculations(args) ⇒ Object 



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# File 'bin/variation_effect_predictor', line 3

def run_calculations(args)
  
  ### GETTING COMMAND LINE PARAMETERS ###
  args.each_index {|x| args.insert(x+1,1) if args[x] == '-h' or args[x] == '-g' } # to have always an even number of parameters
  params = Hash[*args]

  ### PRINT HELP ###
  if params.key?("-h") then
    show_help()
    exit
  end

  ### CHECKING INPUT FILE ###
  if params["-i"].nil? or params == {} then
    show_help()
    puts "\nERROR: You must provide an input file!\n\n"
    exit
  end

  ### SETTING DEFAULT MySQL USER IF NOT SPECIFIED ###
  params["-u"] = "anonymous" if params["-u"].nil?
  params["-P"] = params["-P"].to_i if params["-P"] != nil

  ### OPENING CONNECTION TO ENSEMBL DATABASE ###
  require 'rubygems'
  require 'bio-ensembl'
  include Ensembl::Variation

  if params.key?("-g") then
    params["-d"] = "mysql.ebi.ac.uk" if params["-d"].nil?
    if params["-s"].nil? or params["-r"].nil? then
      puts "\nERROR: For Ensembl Genomes you must provide a valid species and release number!\n\n"
      exit
    end
    DBConnection.ensemblgenomes_connect(params["-s"],params["-r"].to_i,:host => params["-d"], :username => params["-u"],:password => params["-p"],:port => params["-P"])
  else
    params["-s"] = "homo_sapiens" if params["-s"].nil?
    params["-r"] = 60 if params["-r"].nil?
    params["-d"] = "ensembldb.ensembl.org" if params["-d"].nil?
    DBConnection.connect(params["-s"],params["-r"].to_i,:host => params["-d"], :username => params["-u"],:password => params["-p"],:port => params["-P"])
  end

  ### STARTING VARIATIONS PREDICTIONS ###
  File.open(params["-i"]) do |f|
    f.each_line do |l|
      next if l =~ /^#/
      l.chomp!
      data = l.split("\t")
      get_consequence(data[0],data[1],data[2],data[3],data[4],data[5]).each do |tv|
        puts l+"\t Effect: "+tv.consequence_type+" -- "+tv.transcript_stable_id.to_s
      end                       
    end
  end 
end

#show_help ⇒ Object 



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# File 'bin/variation_effect_predictor', line 59

def show_help()
  puts "\nRuby Ensembl API -- Variation Effects Predictor"
  puts "\n\tUSAGE: variation_effect_predictor -i variations.txt [OPTIONS]\n\n"
  puts "\tOPTIONS:\n"
  puts "\t\t-i\t Input file (Tab separated) REQUIRED"
  puts "\t\t-s\t Species in snake case (default is 'homo_sapiens')"
  puts "\t\t-r\t Ensembl Database release (default is 60)"
  puts "\t\t-d\t Ensembl Database Server (default is 'ensembldb.ensembl.org')"
  puts "\t\t-u\t Ensembl Database username (default is 'anonymous')"
  puts "\t\t-p\t Ensembl Database password (only required for local Ensembl database)"
  puts "\t\t-P\t Ensembl Database MySQL port connection (only required for local Ensembl database)"
  puts "\t\t-g\t Connects to Ensembl Genomes Server (default is 'mysql.ebi.ac.uk')"
  puts "\t\t-h\t Show this help"
  puts "\n\n"
end