metagenome_contributions.py – This script partitions metagenome functional contributions according to function, OTU, and sample, for a given OTU table.¶

Description:

Usage: metagenome_contributions.py [options]

Input Arguments:

Note

[REQUIRED]

[OPTIONAL]

-t, --type_of_prediction: Type of functional predictions. Valid choices are: ko, cog, rfam [default: ko]
-g, --gg_version: Version of GreenGenes that was used for OTU picking. Valid choices are: 13_5, 18may2012 [default: 13_5]
-c, --input_count_table: Precalculated function predictions on per otu basis in biom format (can be gzipped). Note: using this option overrides –type_of_prediction and –gg_version. [default: None]
--suppress_subset_loading: Normally, only counts for OTUs present in the sample are loaded. If this flag is passed, the full biom table is loaded. This makes no difference for the analysis, but may result in faster load times (at the cost of more memory usage)
--load_precalc_file_in_biom: Instead of loading the precalculated file in tab-delimited format (with otu ids as row ids and traits as columns) load the data in biom format (with otu as SampleIds and traits as ObservationIds) [default: False]
-l, --limit_to_function: If provided, only output predictions for the specified function ids. Multiple function ids can be passed using comma delimiters.

Output:

Output is a tab-delimited column indicating OTU contribution to each function.

Partition the predicted contribution to the metagenomes from each organism in the given OTU table, limited to only K00001, K00002, and K00004.

metagenome_contributions.py -i normalized_otus.biom -l K00001,K00002,K00004 -o ko_metagenome_contributions.tab

Partition the predicted contribution to the metagenomes from each organism in the given OTU table, limited to only COG0001 and COG0002.

metagenome_contributions.py -i normalized_otus.biom -l COG0001,COG0002 -t cog -o cog_metagenome_contributions.tab