#mkdir lefse_results
format_input.py comp/comparison_3/lefse_L7.txt comp/comparison_3/lefse_results/lefse.in -f c -c 2 -u 1 -o 1000000
run_lefse.py comp/comparison_3/lefse_results/lefse.in  comp/comparison_3/lefse_results/lefse.res > comp/comparison_3/lefse_results/run_lefse.log
plot_res.py  comp/comparison_3/lefse_results/lefse.res comp/comparison_3/lefse_results/lefse.plot.png --format png --title 'Significantly Represented Taxa'
plot_res.py  comp/comparison_3/lefse_results/lefse.res comp/comparison_3/lefse_results/lefse.plot.svg --format svg --title 'Significantly Represented Taxa'
plot_res.py  comp/comparison_3/lefse_results/lefse.res comp/comparison_3/lefse_results/lefse.plot.pdf --format pdf --title 'Significantly Represented Taxa'
plot_cladogram.py comp/comparison_3/lefse_results/lefse.res comp/comparison_3/lefse_results/lefse.cladogram.species.png --format png --title 'Significantly Represented Taxa'
plot_cladogram.py comp/comparison_3/lefse_results/lefse.res comp/comparison_3/lefse_results/lefse.cladogram.species.svg --format svg --title 'Significantly Represented Taxa'
plot_cladogram.py comp/comparison_3/lefse_results/lefse.res comp/comparison_3/lefse_results/lefse.cladogram.species.pdf --format pdf --title 'Significantly Represented Taxa'
plot_cladogram.py comp/comparison_3/lefse_results/lefse.res comp/comparison_3/lefse_results/lefse.cladogram.genus.png --max_lev 6 --format png --title 'Significantly Represented Taxa'
plot_cladogram.py comp/comparison_3/lefse_results/lefse.res comp/comparison_3/lefse_results/lefse.cladogram.genus.svg --max_lev 6 --format svg --title 'Significantly Represented Taxa'
plot_cladogram.py comp/comparison_3/lefse_results/lefse.res comp/comparison_3/lefse_results/lefse.cladogram.genus.pdf --max_lev 6 --format pdf --title 'Significantly Represented Taxa'
plot_features.py comp/comparison_3/lefse_results/lefse.in comp/comparison_3/lefse_results/lefse.res comp/comparison_3/lefse_results/all_diff_features/ -f diff --format png
plot_features.py comp/comparison_3/lefse_results/lefse.in comp/comparison_3/lefse_results/lefse.res comp/comparison_3/lefse_results/all_diff_features/ -f diff --format svg
plot_features.py comp/comparison_3/lefse_results/lefse.in comp/comparison_3/lefse_results/lefse.res comp/comparison_3/lefse_results/all_diff_features/ -f diff --format pdf