1) OTU's annotated by the same taxa are merged and converted to relative abundances
2) Relative taxa abundances are visualized as bar plots
summarize_taxa_through_plots.py -i OTU/otu_table_mc2_w_tax_no_pynast_failures.biom -o Taxa/ -m metadata.csv
Or, to get only relative abundance tables (1) without additional visualization (2)
summarize_taxa.py -i OTU/otu_table_mc2_w_tax_no_pynast_failures.biom -o Taxa/
1) Relative abundance taxa tables
Taxa tables as .biom and .txt format for different taxonomic levels.
ls Taxa/
otu_table_mc2_w_tax_no_pynast_failures_L2.biom # L2 - Phylum
otu_table_mc2_w_tax_no_pynast_failures_L2.txt
otu_table_mc2_w_tax_no_pynast_failures_L3.biom # L3 - Class
otu_table_mc2_w_tax_no_pynast_failures_L3.txt
otu_table_mc2_w_tax_no_pynast_failures_L4.biom # L4 - Order
otu_table_mc2_w_tax_no_pynast_failures_L4.txt
otu_table_mc2_w_tax_no_pynast_failures_L5.biom # L5 - Family
otu_table_mc2_w_tax_no_pynast_failures_L5.txt
otu_table_mc2_w_tax_no_pynast_failures_L6.biom # L6 - Genus
otu_table_mc2_w_tax_no_pynast_failures_L6.txt
2) Relative abundance bar plots for each sample (summarize_taxa_through_plots.py)
Taxa/taxa_summary_plots/bar_charts.html (to open in web-browser)