scale_metagenome.py – This script converts metagenomic relative abundance back to sequence counts, by scaling the relative abundnace of each gene in each sample in a biom file by a user-supplied sequencing depth

Description:

Usage: scale_metagenome.py [options]

Input Arguments:

Note

[REQUIRED]

-s, --input_seq_depth_file

An input tab-delimited table, with samples as the first column and an integer sequencing depth as the second

-i, --input_count_table

The input trait counts on per otu basis in biom format (can be gzipped)

-o, --output_metagenome_table

The output file for the scaled metagenome

Output:

Output is a table of function counts (e.g. KEGG KOs) by sample ids.

Predict metagenomes from genomes.biom and otus.biom.

scale_metagenome.py -i otus.biom -c KEGG_acepic__predict_traits_97.biom.gz -o predicted_metagenomes.biom

Change output format to plain tab-delimited:

scale_metagenome.py -f -i otus.biom -c KEGG_acepic_predict_traits_97.biom.gz -o predicted_metagenomes.tab