summarize_taxa_through_plots.py – A workflow script for performing taxonomy summaries and plots

Description:

The steps performed by this script are:

1. Summarize OTU by Category
2. Summarize Taxonomy
3. Plot Taxonomy Summary

Usage: summarize_taxa_through_plots.py [options]

Input Arguments:

Note

[REQUIRED]

-i, --otu_table_fp

The input otu table [REQUIRED]

-m, --mapping_fp

Path to the mapping file [REQUIRED]

-o, --output_dir

The output directory [REQUIRED]

[OPTIONAL]

-p, --parameter_fp

Path to the parameter file, which specifies changes to the default behavior. See http://www.qiime.org/documentation/file_formats.html#qiime-parameters. [if omitted, default values will be used]

-f, --force

Force overwrite of existing output directory (note: existing files in output_dir will not be removed) [default: None]

-w, --print_only

Print the commands but don’t call them – useful for debugging [default: False]

-c, --mapping_category

Summarize OTU table using this category. [default: None]

Output:

The results of this script is a folder (“wf_taxa_sum/”) containing taxonomy summary files (at different levels) and a folder containing taxonomy summary plots. Additionally, if a mapping_catgory is supplied there will be a summarized OTU table.

Examples:

summarize_taxa_through_plots.py -o wf_taxa_sum -i otu_table.txt -m inseqs1_mapping.txt -p custom_parameters.txt

Alternatively, the user can supply a mapping_category, where the OTU is summarized based on a mapping category:

summarize_taxa_through_plots.py -o wf_taxa_sum -i otu_table.txt -m inseqs1_mapping.txt -p custom_parameters.txt -c Treatment