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Contents
module Lederhosen
class CLI
##
# PAIRED-END READ WORK-AROUND (JOIN THEM)
#
desc "join",
"join trimmed reads into a single file"
method_option :trimmed, :type => :string, :required => true
method_option :output, :type => :string, :required => true
def join
trimmed = Dir[options[:trimmed]]
output = options[:output]
ohai "joining #{File.dirname(trimmed.first)} saving to #{output}"
ohno "no reads in #{trimmed}" if trimmed.length == 0
output = File.open(output, 'w')
pbar = ProgressBar.new "joining", trimmed.length
trimmed.each do |fasta_file|
pbar.inc
begin
records = Dna.new File.open(fasta_file)
rescue
ohai "skipping #{fasta_file} (empty?)"
next
end
records.each_slice(2) do |l, r|
output.puts ">#{r.name}:split=#{r.sequence.size}:sample=#{File.basename(fasta_file, '.fasta')}\n#{r.sequence.reverse+l.sequence}"
end
end
pbar.finish
end
end
end
Version data entries
7 entries across 7 versions & 1 rubygems