shared_phylotypes.py – Compute shared OTUs between all pairs of samples

Description:

This script computes from an OTU table a matrix with the number of shared phylotypes between all pairs of samples.

Usage: shared_phylotypes.py [options]

Input Arguments:

Note

[REQUIRED]

-i, --otu_table_fp

Path to the input OTU table or a directory containing (only) OTU tables

-o, --output_fp

The output filepath

[OPTIONAL]

-r, --reference_sample

Name of reference sample to which all pairs of samples should be compared [default: None]

-f, --force_overwrite

Overwrite output_fp if already exists [default: None]

Output:

Single file example:

Compute shared OTUs on one OTU table

shared_phylotypes.py -i otu_table.txt -o shared_otus.txt

Reference sample example:

Compute shared OTUs with respect to a reference sample. Computes shared OTUs between all pairs of samples and the reference sample. E.g. in a transplant study this can be used to establish a base line count of shared OTUs with the Donor sample before and after the transplant.

shared_phylotypes.py -i otu_table.txt -o shared_otus.txt -r Sample_X

Batch mode example:

Compute shared OTUs for a set of OTU tables, e.g. from running multiple_rarefactions.py, with an even number of sequences per sample. The resulting directory can be fed to dissimilarity_mtx_stats.py, which computes mean, median and the standard deviation on the provided tables.

shared_phylotypes.py -i rarefaction_out/ -o rarefied_shared_otus/