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Contents
##
# FINALLY, CLUSTER!
#
module Lederhosen
class CLI
desc "cluster",
"cluster a fasta file using UCLUST"
method_option :input, :type => :string, :required => true
method_option :output, :type => :string, :required => true
method_option :identity, :type => :numeric, :required => true
method_option :stepwords, :type => :numeric, :default => 8
method_option :wordlen, :type => :numeric, :default => 8
method_option :maxaccepts, :type => :numeric, :default => 1
method_option :maxrejects, :type => :numeric, :default => 8
method_option :lib, :type => :string
def cluster
identity = options[:identity]
output = options[:output]
input = options[:input]
stepwords = options[:stepwords]
maxaccepts = options[:maxaccepts]
maxrejects = options[:maxrejects]
wordlen = options[:wordlen]
lib = options[:lib]
ohai "clustering #{input}, saving to #{output}"
options.each_pair do |key, value|
ohai "#{key} = #{value}"
end
cmd = [
'uclust',
"--input #{input}",
"--uc #{output}",
"--id #{identity}",
"--stepwords #{stepwords}",
"--maxaccepts #{maxaccepts}",
"--maxrejects #{maxrejects}",
"--w #{wordlen}"
]
cmd << "--lib #{lib}" unless lib.nil?
cmd = cmd.join(' ')
@shell.mute { run cmd }
end
end
end
Version data entries
21 entries across 21 versions & 1 rubygems