picrust/picrust — pull request #66 by zaneveld (2013-01-11 00:53:07+00:00)
Title: Metagenome contributions

Addresses Issue #62 by adding code to detect the contribution of each organism to a given function.

Right now this is slow for large datasets. I included a limit_to_function option which allows for specifying only a comma-separated list of gene functions.

Output is a tab delimited file listing the function, sample, organism, the organisms contribution to the function in the sample and across all samples, and how that contribution is made up (number of organisms inferred, copy number, total contribution).

New scripts:
-- metagenome_contributions.py (script and library)
-- test_metagenome_contributions.py

To run on test data:
metagenome_contributions.py -i test_otu_table_with_metadata_normalized.biom -c test_otu_table_marker_gene_counts.biom -o test_metagenome_contributions.tsv

To run on test data limiting to only gene function f1:
metagenome_contributions.py -i test_otu_table_with_metadata_normalized.biom -c test_otu_table_marker_gene_counts.biom -o test_metagenome_contributions.tsv --limit_to_function f1

Later changes may want to hook this up with the subset loader, but that will only happen after both pull requests are merged so I'm putting it off for now.