Sha256: 28b6f5f518735dac3322443705d6b4ea180c23a32029af0ea997e95c18c954ad
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Size: 1.5 KB
Versions: 33
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Stored size: 1.5 KB
Contents
require 'set'
module Lederhosen
class CLI
desc 'join_otu_tables', 'combine multiple otu tables'
method_option :input, :type => :string, :required => true
method_option :output, :type => :string, :required => true
def join_otu_tables
input = Dir[options[:input]]
output = File.expand_path(options[:output])
ohai "combining #{input.size} file(s) and saving to #{output}"
all_otu_names = Set.new
all_samples = Set.new
sample_name_count = Hash.new { |h, k| h[k] = Hash.new { |h, k| h[k] = 0 } }
# read all of the csv files
input.each do |input_file|
File.open(input_file) do |handle|
otu_names = handle.gets.strip.split(',')[1..-1]
all_otu_names += otu_names.to_set
handle.each do |line|
line = line.strip.split(',')
sample = File.basename(input_file)
all_samples << sample
read_counts = line[1..-1]
otu_names.zip(read_counts) do |name, count|
sample_name_count[sample][name] = count
end
end
end
end
# save to csv
File.open(output, 'w') do |handle|
header = all_otu_names.to_a.sort
handle.puts "-,#{header.join(',')}"
all_samples.to_a.sort.each do |sample|
handle.print "#{sample}"
header.each do |name|
handle.print ",#{sample_name_count[sample][name]}"
end
handle.print "\n"
end
end
end
end
end
Version data entries
33 entries across 33 versions & 1 rubygems