Sha256: c4ed7ce9aeb2d4eb1006ec2d965b53dd565b056ddb746642d6b6cb9900fbf7e8
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Size: 901 Bytes
Versions: 24
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Stored size: 901 Bytes
Contents
##
# QUALITY TRIMMING
#
module Lederhosen
class CLI
desc "trim",
"trim reads based on quality scores"
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]
ohai "trimming #{File.dirname(raw_reads)} and saving to #{out_dir}"
run "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
24 entries across 24 versions & 1 rubygems