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Contents
##
# MAKE TABLES
#
module Lederhosen
class CLI
desc "otu_table",
"create an OTU abundance matrix from taxonomy count files"
method_option :files, :type => :string, :required => true
method_option :level, :type => :string, :required => true
method_option :output, :type => :string, :required => true
def otu_table
inputs = Dir[options[:files]]
level = options[:level].downcase
output = options[:output]
ohai "Generating OTU matrix from #{inputs.size} inputs at #{level} level and saving to #{output}."
# sanity check
fail "bad level: #{level}" unless %w{domain phylum class order family genus species kingdom original}.include? level
fail 'no inputs matched your glob' if inputs.size == 0
sample_cluster_count = Hash.new { |h, k| h[k] = Hash.new { |h, k| h[k] = 0 } }
# create a progress bar with the total number of bytes of
# the files we're slurping up
pbar = ProgressBar.new "loading", inputs.size
inputs.each do |input_file|
File.open(input_file).each do |line|
next if line =~ /^#/ # skip header(s)
line = line.strip.split(',')
taxonomy, count = line
count = count.to_i
tax =
if taxonomy == 'unclassified_reads'
'unclassified_reads'
else
parse_taxonomy(taxonomy)[level]
end
sample_cluster_count[input_file][tax] += count
end
pbar.inc
end
pbar.finish
all_clusters = sample_cluster_count.values.map(&:keys).flatten.uniq.sort
out = File.open(output, 'w')
out.puts all_clusters.join(',')
inputs.sort.each do |input|
out.print "#{input}"
all_clusters.each do |c|
out.print ",#{sample_cluster_count[input][c]}"
end
out.print "\n"
end
end
end # class CLI
end # module Lederhosen
Version data entries
4 entries across 4 versions & 1 rubygems