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Versions: 12
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Contents
require 'set'
module Lederhosen
class CLI
desc 'get_reps', 'get representative reads for a uc file'
method_option :input, :type => :string, :required => true
method_option :database, :type => :string, :required => true
method_option :output, :type => :string, :required => true
def get_reps
inputs = Dir[options[:input]]
database = File.expand_path(options[:database])
output = File.expand_path(options[:output])
taxa = Set.new
ohai "getting representative database sequences from #{database} using #{inputs.size} cluster file(s) and saving to #{output}"
# parse uc file, get list of taxa we need to get
# full sequences for from the database
pbar = ProgressBar.new 'reading uc(s)', inputs.size
inputs.each do |input|
File.open(input) do |handle|
results = UCParser.new(handle)
results.each do |result|
taxa << result.target if result.hit?
end
end
end
pbar.finish
ohai "found #{taxa.size} representative sequences"
# print representative sequences from database
output = File.open(output, 'w')
kept = 0
File.open(database) do |handle|
Dna.new(handle).each do |record|
if taxa.include? record.name
output.puts record
kept += 1
end
end
end
output.close
ohai "saved #{kept} representatives"
end
end
end
Version data entries
12 entries across 12 versions & 1 rubygems