– 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


Usage: [options]

Input Arguments:



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

Predict metagenomes from genomes.biom and otus.biom. -i otus.biom -c KEGG_acepic__predict_traits_97.biom.gz -o predicted_metagenomes.biom

Change output format to plain tab-delimited: -f -i otus.biom -c KEGG_acepic_predict_traits_97.biom.gz -o