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Contents
##
# GET REPRESENTATIVE READS
#
module Lederhosen
class CLI
desc "rep_reads",
"output a fasta file containing representative reads for each cluster given a UCLUST output file and the joined reads file"
method_option :clusters, :type => :string, :required => true
method_option :output, :type => :string, :required => true
method_option :joined, :type => :string, :required => true
def rep_reads
input = options[:clusters]
output = options[:output]
joined_reads = options[:joined]
ohai "getting represntative reads for #{input} w/ reads #{joined_reads} and saving to #{output}"
# Load cluster table!
clstr_info = Helpers.load_uc_file input
clstr_counts = clstr_info[:clstr_counts] # clstr_counts[:clstr][sample.to_i] = reads
seed_to_clstrnr = clstr_info[:seed_to_clstrnr]
samples = clstr_info[:samples]
out_handle = File.open("#{output}", 'w')
File.open(joined_reads) do |handle|
records = Dna.new handle
records.each do |dna|
clstrnr = seed_to_clstrnr[dna.name]
unless clstrnr.nil?
dna.name = "#{dna.name}:cluster-#{clstrnr}"
out_handle.puts dna
end
end
end
out_handle.close
end
end
end
Version data entries
24 entries across 24 versions & 1 rubygems