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Merging several DADA2 denoised run feature tables and representative sequences for Qiime version 2017.12
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#!/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' |
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