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 the 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_dir

Path to the output directory

-d, --dissim

Dissimilarity between nodes up the tree, as a single value or comma-separated list of values

-n, --num

Number of simulated samples per input sample, as a single value or comma-separated list of values

[OPTIONAL]

-m, --mapping_fp

The mapping filepath. If provided, an output mapping file containing the replicated sample IDs (with all other metadata columns copied over) will also be created [default: None]

Output:

The output directory will contain an OTU table with samples named: ‘original_sample_0, original_sample_1 ...’

If a mapping file is provided via -m, an output mapping file containing the replicated sample IDs (with all other metadata columns copied over) will also be created.

Create an OTU table with 3 related samples for each sample in otu_table.biom with dissimilarities of 0.001.

simsam.py -i otu_table.biom -t rep_set.tre -o simsam_out1 -d .001 -n 3

Create OTU tables with 2, 3 and 4 related samples for each sample in otu_table.biom with dissimilarities of 0.001 and 0.01. Additionally create new mapping files with metadata for each of the new samples for use in downstream analyses.

simsam.py -i otu_table.biom -t rep_set.tre -o simsam_out2 -d .001,.01 -n 2,3,4 -m map.txt