Sha256: 73cbd1c44fc5cb0f3d5e735875502a91b46649bdfd47aa685296abdac547116d
Contents?: true
Size: 728 Bytes
Versions: 17
Compression:
Stored size: 728 Bytes
Contents
require 'bio-faster'
require 'parallel'
module Bio
class Gadget < Thor
namespace :bio
desc 'dedup', 'deduplicate fastq (via STDIN)'
def dedup
p1in, p1out = IO.pipe
fork {
p1in.close
$stdout.reopen(p1out)
open("| sort -k 1 -r -S #{sprintf('%2d', 100/(Parallel.processor_count+1))}% -T $TMPDIR | cut -f 2- | uniq -f 2", 'w') { |fp|
Bio::Faster.new(:stdin).each_record(:quality => :raw) do |seqid, seq, qvs|
fp.puts "#{seq}#{qvs}\t#{seqid}\t#{qvs}\t#{seq}"
end
}
}
p1out.close
p1in.each_line { |line|
seqid, qvs, seq = line.rstrip.split
puts "@#{seqid}\n#{seq}\n+\n#{qvs}"
}
end
end
end
Version data entries
17 entries across 17 versions & 1 rubygems