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Contents
require_relative "SNP"
require 'bio-samtools'
module Bio::PolyploidTools
class SNPSequenceException < RuntimeError
end
class SNPSequence < SNP
attr_accessor :sequence_original
#Format:
#snp name,chromsome from contig,microarray sequence
#BS00068396_51,2AS,CGAAGCGATCCTACTACATTGCGTTCCTTTCCCACTCCCAGGTCCCCCTA[T/C]ATGCAGGATCTTGATTAGTCGTGTGAACAACTGAAATTTGAGCGCCACAA
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 = reg_str.split(",")
elsif arr.size == 2
snp.gene, snp.sequence_original = arr
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.exon_list = Hash.new()
snp
end
def parse_snp
end
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
end
end
Version data entries
10 entries across 10 versions & 1 rubygems