normalize_by_copy_number.py – Normalize an OTU table by marker gene copy number — PICRUSt 1.1.4 documentation (original) (raw)

Description:

Usage: normalize_by_copy_number.py [options]

Input Arguments:

Note

[REQUIRED]

-i, --input_otu_fp

The input otu table filepath in biom format

-o, --output_otu_fp

The output otu table filepath in biom format

[OPTIONAL]

-g, --gg_version

Version of GreenGenes that was used for OTU picking. Valid choices are: 13_5, 18may2012 [default: 13_5]

-c, --input_count_fp

Precalculated input marker gene copy number predictions on per otu basis in biom format (can be gzipped).Note: using this option overrides –gg_version. [default: None]

--metadata_identifer

Identifier for copy number entry as observation metadata [default: CopyNumber]

--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]

Output:

A normalized OTU table

Normalize the OTU abundances for a given OTU table picked against the newest version of Greengenes:

normalize_by_copy_number.py -i closed_picked_otus.biom -o normalized_otus.biom

Change the version of Greengenes used for OTU picking:

normalize_by_copy_number.py -g 18may2012 -i closed_picked_otus.biom -o normalized_otus.biom