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Contents
module Lederhosen
class CLI
##
# PAIRED-END READ WORK-AROUND (JOIN THEM)
#
desc "join",
"join paired or unpaired reads into a single file. Paired reads are joined end-to-end"
method_option :trimmed, :type => :string, :required => true
method_option :output, :type => :string, :required => true
method_option :paired, :type => :boolean, :default => true
def join
trimmed = Dir[options[:trimmed]]
output = options[:output]
paired = options[:paired]
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
records =
begin
Dna.new File.open(fasta_file)
rescue
ohai "skipping #{fasta_file} (empty?)"
next
end
if paired
output_paired_reads(records, output, fasta_file)
else
output_unpaired_reads(records, output, fasta_file)
end
end
pbar.finish
end
no_tasks do
##
# Output paired reads joined together
#
def output_paired_reads(records, output, fasta_file)
records.each_slice(2) do |l, r|
output.puts ">#{r.name}:split=#{r.sequence.size}:sample=#{File.basename(fasta_file, '.fasta')}"
output.puts "#{r.sequence.reverse+l.sequence}"
end
end
##
# Output unpaired reads
#
def output_unpaired_reads(records, output, fasta_file)
records.each do |r|
output.puts ">#{r.name}:split=na:sample=#{File.basename(fasta_file, '.fasta')}"
output.puts r.sequence
end
end
end
end
end
Version data entries
8 entries across 8 versions & 1 rubygems