class Bio::PolyploidTools::SNPSequence
Attributes
sequence_original[RW]
Public Class Methods
parse(reg_str)
click to toggle source
Format: snp name,chromsome from contig,microarray sequence BS00068396_51,2AS,CGAAGCGATCCTACTACATTGCGTTCCTTTCCCACTCCCAGGTCCCCCTAATGCAGGATCTTGATTAGTCGTGTGAACAACTGAAATTTGAGCGCCACAA
# 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
Public Instance Methods
parse_sequence_snp()
click to toggle source
# File lib/bio/PolyploidTools/SNPSequence.rb, line 37 def parse_sequence_snp pos = 0 match_data = /(?<pre>\w*)\[(?<org>[ACGT])\/(?<snp>[ACGT])\](?<pos>\w*)/.match(sequence_original.strip) if match_data @position = Regexp.last_match(:pre).size + 1 @original = Regexp.last_match(:org) @snp = Regexp.last_match(:snp) amb_base = Bio::NucleicAcid.to_IUAPC("#{@original}#{@snp}") @template_sequence = "#{Regexp.last_match(:pre)}#{amb_base}#{Regexp.last_match(:pos)}" end end