Sha256: 8e6df3aa53ba7b6465f632cd4ab8e017f3a086c99313134ffc10b2d3f1620dbd
Contents?: true
Size: 820 Bytes
Versions: 20
Compression:
Stored size: 820 Bytes
Contents
module Bio
class Gadget < Thor
namespace :bio
desc 'qvstat QUAL', 'statistics of quality values in *.qual file'
def qvstat(qualfile)
stat = Hash.new
myopen(qualfile) { |fp|
fp.each { |line|
next if /^[\#\>]/ =~ line
qvs = line.rstrip.split
qvs.each_index { |i|
qv = qvs[i]
stat[qv] = Array.new unless stat.key?(qv)
if stat[qv][i].nil?
stat[qv][i] = 1
else
stat[qv][i] += 1
end
}
}
}
statfile = qualfile.sub(/.qual(.gz)?$/, '.qvstat')
open(statfile, 'w') { |out|
qvs = stat.keys.sort { |a, b| a.to_i <=> b.to_i }
qvs.each { |qv|
out.puts "#{qv} #{stat[qv].join(' ')}"
}
}
end
end
end
Version data entries
20 entries across 20 versions & 1 rubygems