Contents

##
# QUALITY TRIMMING
#

module Lederhosen
  class CLI

    desc "trim Illumina QSEQ files",
         "--reads_dir=reads/* --out_dir=trimmed.fasta"

    method_option :reads_dir, :type => :string, :required => true
    method_option :out_dir,   :type => :string, :required => true

    def trim

      raw_reads = options[:reads_dir]
      out_dir = options[:out_dir]

      `mkdir -p #{out_dir}`

      raw_reads = Helpers.get_grouped_qseq_files raw_reads
      ohai "found #{raw_reads.length} pairs of reads"

      pbar = ProgressBar.new "trimming", raw_reads.length

      raw_reads.each do |a|
        pbar.inc
        out = File.join(out_dir, "#{File.basename(a[0])}.fasta")
        # TODO get total and trimmed
        total, trimmed = Helpers.trim_pairs a[1][0], a[1][1], out, :min_length => 70
      end

      pbar.finish
    end
  end
end

Version data entries

6 entries across 6 versions & 1 rubygems

Version	Path
lederhosen-0.1.2	lib/lederhosen/tasks/trim.rb
lederhosen-0.1.1	lib/lederhosen/tasks/trim.rb
lederhosen-0.1.0	lib/lederhosen/tasks/trim.rb
lederhosen-0.0.11	lib/lederhosen/tasks/trim.rb
lederhosen-0.0.10	lib/lederhosen/tasks/trim.rb
lederhosen-0.0.9	lib/lederhosen/tasks/trim.rb