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Contents
##
# MAKE TABLES
#
SEP = ','
module Lederhosen
class CLI
desc "otu_table",
"create an OTU abundance matrix from UCLUST output"
method_option :clusters, :type => :string, :required => true
method_option :output, :type => :string, :required => true
def otu_table
input = options[:clusters]
output = options[:output]
ohai "generating otu table from #{input}, 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
clstrnr_to_seed = clstr_info[:clstrnr_to_seed]
samples = clstr_info[:samples]
# print OTU abundance matrix
# clusters as columns
# samples as rows
File.open("#{output}", 'w') do |h|
samples = samples.sort
clusters = clstr_counts.keys
# print header (cluster names)
h.puts '-' + SEP + clusters.map { |x| "cluster-#{x}" }.join(SEP)
samples.each do |sample|
h.print sample
clusters.each do |cluster|
h.print "#{SEP}#{clstr_counts[cluster][sample]}"
end
h.print "\n"
end
end
end
end
end
Version data entries
22 entries across 22 versions & 1 rubygems