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Tool to merge 23andme and Ancestory.com raw dna files
#!/usr/bin/ruby
#
# Usage:
# ruby ./merge_dna_files.rb file,file1,file2... > merged_file.txt
#
# Example:
# ruby ./merge_dna_files.rb AncestryDNA.txt genome_John_Doe_v4_Full_20170428065226.txt > merged_raw.txt
#
# Supports 23andMe, AncestryDNA, and Genes for Good 23andMe compatible file formats.
# The result will be in 23andMe file format.
#
def flip_val(val)
{
'G' => 'C',
'T' => 'A'
}[val] || val
end
def is_values_equal(val1, val2)
val1, val2 = [val1, val2].map{|val| val.size == 1 ? (val + val) : val }
val1.split('').map{|v| flip_val(v) }.sort == val2.split('').map{|v| flip_val(v) }.sort
end
def select_record(existing_record, new_record)
if !is_values_equal(existing_record[:val], new_record[:val])
$stderr.puts "Conflict for #{new_record[:snp_id]}: #{new_record[:file]} vs #{existing_record[:file]}, values #{new_record[:val]} vs #{existing_record[:val]}"
end
# Priority for 23andMe and Genes for Good formats
selected_record = [new_record, existing_record].find {|record| ['23andMe', 'Genes for Good'].include?(record[:type]) }
return selected_record || new_record
end
$snps = {}
$stat = {}
$intersections = 0
source_files = ARGV
source_files.each do |file|
type = nil
File.readlines(file).each do |line|
if line.strip[0] == '#'
type = 'ancestry' if line.include?("AncestryDNA")
type = '23andMe' if line.include?("23andMe")
type = 'Genes for Good' if line.include?("Genes for Good")
next
end
snp = line.strip.split("\t")
snp_id = snp[0]
position = snp[2]
chr = snp[1]
val = snp[3]
val += snp[4] if snp[4] # Ancestry values format
next if snp_id == 'rsid' # Ancestry file format first uncommented string
next if ['--', '00'].include?(val) # no call or void result
# Convert Ancestry chrs to 23andMe format
chr = {'23' => 'X', '24' => 'Y', '25' => 'X', '26' => 'MT'}[chr] || chr
new_recod = {
snp_id: snp_id,
chr: chr,
position: position,
val: val,
type: type,
file: file
}
$stat[file] ||= 0
$stat[file] += 1
if existing_record = $snps[snp_id]
$intersections += 1
$snps[snp_id] = select_record(existing_record, new_recod)
else
$snps[snp_id] = new_recod
end
end
end
$stderr.puts "#{$intersections} intersections found."
puts "#DNA raw data file merged from:"
$stat.each do |file, snp_count|
puts "# #{file} with #{snp_count} SNPs"
end
puts "# #{$intersections} intersections were found among these files."
puts "#"
puts "# rsid chromosome position genotype"
$snps.each do |key,values|
puts "#{key}\t#{values[:chr]}\t#{values[:position]}\t#{values[:val]}"
end
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