vamb-abundance-profile 0.0.3

A very simple package to convert the output of VAMB to an abundance table

VAMB abundance profile

This is a small package to create an abundance profile from a VAMB output.

We assume that you have already run VAMB and have the output files, and we read the abundance.npz file and composition.npz files to create a table with the abundance of each contig in each sample.

We append the cluster information from vae_clusters.tsv to the table.

Next, we use the first dimnension of a PCA to reduce the dimensionality of the data so that we end up with a single abundance profile for each cluster.

You can write the final abundance profile to a file using the required --cluster option, and you can also write the intermediate table to a file using the optional --abundance option.

Installation

You can install the package using pip:

pip install vamb-abundance-profile

Usage

Note that by default the vamb directory is in the output directory you specified when running VAMB. That directory should contain the abundance.npz, composition.npz, and vae_clusters.tsv files.

vamb_abundance_profile --vamb vamb/vamb/ --cluster vamb/clusters.tsv.gz -v

Output

The output is a tab-separated file with the abundance profile of each cluster in each sample.

Note that by default we use gzip compression. If your file names do not end .gz, we add that for you! If you don't want compression, then uncompress the file after running the script.