restrict_repset.py

Take a subset BIOM table (e.g. from a core calculation) and a representative set (repset) FASTA file and create a new repset restricted to the OTUs in the BIOM table.

usage: restrict_repset.py [-h] -i BIOM_FP -r REPSET_FP [-o REPSET_OUT_FP]

Required arguments

-i BIOM_FP, --biom_fp BIOM_FP

Path to a biom-format file with OTU-Sample abundance data.

-r REPSET_FP, --repset_fp REPSET_FP

Path to a FASTA-format file containing the representative set of OTUs.

Optional arguments

-o REPSET_OUT_FP, --repset_out_fp REPSET_OUT_FP

Path to the new restricted repset file.

-h, --help

Show the help message and exit