simsam.py – Simulate samples for each sample in an OTU table, using a phylogenetic tree.

Description:

This script makes n samples related to each sample in an input otu table

An input OTU table with 3 samples and n=2 will result in an output otu table with 6 samples total: 3 clusters of 2 related samples.

To simulate each of new samples, this script uses a sample in the input OTU table, and for each OTU in that sample the script traverses rootward on the tree a distance specified by ‘-d’ to a point x. It then randomly selects a tip that decends from x, (call that new tip ‘o2’), and reassigns all observations of the original OTU to the tip/OTU ‘o2’.

Usage: simsam.py [options]

Input Arguments:

Note

[REQUIRED]

-i, --otu_table

The input otu table

-t, --tree_file

Tree file

-o, --output_file

The output file

-d, --dissim

Dissimilarity between nodes up the tree

-n, --num

Number of simulated samples per input sample

Output:

an otu table, samples are named: ‘original_sample_0, original_sample_1 ...’

Make 3 related sample for each sample in otu_table.biom.

simsam.py -i otu_table.biom -t rep_set.tre -o otu_table.simsam.biom -d .001 -n 3