download_picrust_files.py – Download PICRUSt precalculated files

Description:

Downloads the PICRUSt precalculated files and stores them in the PICRUSt data directory.

Note that the script will skip downloading files already in the data directory (unless the --force argument is used).

Usage: download_picrust_files.py [options]

Input Arguments:

Note

[OPTIONAL]

--force

Download the files again (i.e. overwrite any existing ones) [default: False]

-g, --gg_version

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

-t, --type_of_prediction

Type of functional predictions. Valid choices are: ko, cog, rfam [default: ko]

--with_confidence

Download the precalculated files that allow confidence interval calculations for metagenome predictions. Only available for GreenGenes 13_5. [default: False]

Output:

Files are downloaded and stored in PICRUSt’s internally used data directory.

Download the default files (GreenGenes 13_5, KEGG KOs):

download_picrust_files.py

Download the default files (GreenGenes 13_5, KEGG KOs) and the files necessary for calculating confidence intervals:

download_picrust_files.py --with_confidence

Use GreenGenes 18may2012 and COG:

download_picrust_files.py -g 18may2012 -t cog