class Bio::DB::Primer3::KASPContainer

Attributes

line_1[RW]
line_2[RW]
scores[RW]
snp_hash[RW]

Public Instance Methods

add_primers_file(filename) click to toggle source
# File lib/bio/db/primer3.rb, line 790
def add_primers_file(filename)
  #primer3record.scores = @scores if @scores
  Primer3Record.parse_file(filename, scores: @scores) do | primer3record |
    current_snp = @snp_hash["#{primer3record.snp.to_s}:#{primer3record.chromosome}"]
    current_snp.add_record(primer3record)
  end
end
add_snp(snp_in) click to toggle source
# File lib/bio/db/primer3.rb, line 769
def add_snp(snp_in) 
  #TODO: Here we need to also copy the errors that will be printed.
  @snp_hash=Hash.new unless @snp_hash
  snp = SNP.new
  snp.gene = snp_in.gene
  snp.original = snp_in.original
  snp.primer3_errors = Set.new snp_in.errors
  snp.position = snp_in.position
  snp.snp = snp_in.snp
  snp.repetitive = snp_in.repetitive
  #puts snp_in.inspect
  snp.hit_count = snp_in.hit_count
  snp.snp_type  = snp_in.snp_type
  snp.line_1 = @line_1
  snp.line_2 = @line_2 
  snp.snp_from = snp_in
  snp.regions = snp_in.exon_list.values.collect { |x|  x.collect {|y| y.target_region.to_s }}
  @snp_hash[snp.to_s] = snp
  snp
end
add_snp_file(filename) click to toggle source
# File lib/bio/db/primer3.rb, line 760
def add_snp_file(filename)
  @snp_hash=Hash.new unless @snp_hash
  SNP.parse_file(filename) do |snp|
    @snp_hash[snp.to_s] = snp
    snp.line_1 = @line_1
    snp.line_2 = @line_2
  end
end
print_primers() click to toggle source
print_primers_with_tails(tail_a: "GAAGGTCGGAGTCAACGGATT", tail_b: "GAAGGTGACCAAGTTCATGCT") click to toggle source