compare_biom.py – Compare the accuracy of biom files (expected and observed) either by observations (default) or by samples.

Description:

Usage: compare_biom.py [options]

Input Arguments:

Note

[REQUIRED]

-e, --exp_trait_table_fp

The expected trait table (biom format)

-o, --output_fp

The output file

[OPTIONAL]

-c, --compare_observations

Calculate accuracy values by comparing between observations (instead of between samples) [default: False]

-n, --normalize

Convert both expected and observed tables to relative abundances (instead of observations) [default: False]

-l, --limit_to_expected_observations

Ignore observations that are not in the expected table[default: False]

--limit_to_observed_observations

Ignore observations that are not in the observed table[default: False]

-s, --shuffle_samples

Shuffle samples ids randomly before measuring accuracy[default: False]

--not_relative_abundance_scores

Round numbers (instead of taking ceil() which is used for RA) before calculating TP,FP,FN,TN [default: False]

Output:

Outputs will be tab delimited file with various accuracy metrics.

Example 1:

Compare an observed table to an expected table using relative abundance

compare_biom.py -e expected_ra.biom -o compare_results_ra.tab observed_ra.biom

Example 2:

Compare an observed table to an expected table using real counts

compare_biom.py --not_relative_abundance -e expected.biom -o compare_results.tab observed.biom