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Versions: 7
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Contents
module Lederhosen
class CLI
desc 'cluster', 'reference-based clustering using usearch'
method_option :input, :type => :string, :required => true
method_option :database, :type => :string, :required => true
method_option :threads, :type => :numeric, :default => 0
method_option :identity, :type => :numeric, :required => true
method_option :output, :type => :string, :required => true
method_option :strand, :type => :string, :default => 'plus'
def cluster
input = options[:input]
database = options[:database]
threads = options[:threads]
identity = options[:identity]
output = options[:output]
strand = options[:strand]
ohai "clustering #{input} to #{database} and saving to #{output}"
options.each_pair do |key, value|
ohai "#{key} = #{value}"
end
cmd = ['usearch',
"--usearch_local #{input}",
"--id #{identity}",
"--uc #{output}",
"--db #{database}",
"--strand #{strand}"
]
# threads = 0 : use all threads (default)
if threads != 0
cmd << "--threads #{threads}"
end
cmd = cmd.join(' ')
run cmd
end
end
end
Version data entries
7 entries across 7 versions & 1 rubygems