Method: Bio::PolyploidTools::SNPSequence.parse

Defined in:
lib/bio/PolyploidTools/SNPSequence.rb

.parse(reg_str) ⇒ Object

Format: snp name,chromsome from contig,microarray sequence BS00068396_51,2AS,CGAAGCGATCCTACTACATTGCGTTCCTTTCCCACTCCCAGGTCCCCCTAATGCAGGATCTTGATTAGTCGTGTGAACAACTGAAATTTGAGCGCCACAA



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# File 'lib/bio/PolyploidTools/SNPSequence.rb', line 14

def self.parse(reg_str)
  reg_str.chomp!
  snp = SNPSequence.new

  arr = reg_str.split(",")
  
  if arr.size == 3
    snp.gene, snp.chromosome, snp.sequence_original = arr
  elsif arr.size == 2
   snp.gene, snp.sequence_original = arr
   snp.chromosome = ""
 else
   throw SNPSequenceException.new "Need two or three fields to parse, and got #{arr.size} in #{reg_str}"
  end
  #snp.position = snp.position.to_i
  #snp.original.upcase!
  #snp.snp.upcase!  
  snp.chromosome. strip!
  snp.parse_sequence_snp
  
  snp
end