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Contents
module Lederhosen
class CLI
desc 'otu_filter', 'works like uc_filter but uses an OTU table as input'
method_option :input, :type => :string, :required => true
method_option :output, :type => :string, :required => true
method_option :reads, :type => :numeric, :required => true
method_option :samples, :type => :numeric, :required => true
def otu_filter
input = options[:input]
output = options[:output]
reads = options[:reads]
samples = options[:samples]
ohai "filtering otu file #{input} (reads = #{reads}, samples = #{samples}), saving to #{output}"
##
# Iterate over otu table line by line.
# Only print if cluster meets criteria
#
kept = 0
File.open(input) do |handle|
header = handle.gets.strip
header = header.split(',')
samples = header[1..-1]
puts header.join(',')
handle.each do |line|
line = line.strip.split(',')
cluster_no = line[0]
counts = line[1..-1].collect { |x| x.to_i }
# should be the same as uc_filter
if counts.reject { |x| x < reads }.length > samples
puts line.join(',')
kept += 1
end
end
end
ohai "kept #{kept} clusters."
end
end
end
Version data entries
9 entries across 9 versions & 1 rubygems