Sha256: 3ee0b7b44a9322a5314730e2ef8170c3db1870949e17975c13b8565fda804d65
Contents?: true
Size: 809 Bytes
Versions: 17
Compression:
Stored size: 809 Bytes
Contents
require 'parallel'
require 'pathname'
module Bio
class Gadget < Thor
namespace :bio
desc 'fqxz', 'automatic (re)compression of *.fq(.gz|.bz2) files'
def fqxz
Parallel.map(Pathname.glob('*.fq{.gz,.bz2,}')) { |fqfilename|
xzfilename = fqfilename.sub(/\.fq(\.(gz|bz2))*$/, '.fq.xz')
if !xzfilename.exist?
case fqfilename.extname
when '.gz'
decompressor = 'gunzip -c'
when '.bz2'
decompressor = 'bunzip2 -c'
else
decompressor = 'cat'
end
puts "compressing #{xzfilename}..."
system "#{decompressor} #{fqfilename} | xz -z -e -c > #{xzfilename} 2> #{xzfilename}.log"
system "xz -t #{xzfilename} >> #{xzfilename}.log 2>&1"
end
}
end
end
end
Version data entries
17 entries across 17 versions & 1 rubygems