#!/usr/bin/env ruby
# Qiime2: Merging several DADA2 denoised run feature tables and representative sequences for Qiime version 2017.12
# Feature tables must be name *_table.qza and representative sequences *_rep-seqs.qza
# V1.00 Written by Gisle Vestergaard

require 'pp'
require 'optparse'

tables = []
seqs   = []

table = `ls | grep _table.qza`
table.each_line do |line|
  line.chomp!
  tables << line
end

seq = `ls | grep _rep-seqs.qza`
seq.each_line do |line|
  line.chomp!
  seqs << line
end

system 'qiime feature-table merge --i-tables ' + tables.each {|x| x}.join(" --i-tables ") + ' --o-merged-table merged_table.qza'
system 'qiime feature-table merge-seqs --i-data ' + seqs.each {|x| x}.join(" --i-data ") + ' --o-merged-data merged_rep-seqs.qza'