filter_keep_otus_by_sample

This filter allows for the removal of sequences not contained within a user- specified list of Sample IDs. This script examines each OTU and removes any sequences not originating from the specified set of allowed Sample IDs. Any empty OTUs that result are removed.

usage: filter_keep_otus_by_sample.py [-h] -i OTU_MAP -k SAMPLES_TO_KEEP_FP -o OUTPUT_OTU_MAP_FP [-v]

Required Arguments

-i OTU_MAP, --otu_map OTU_MAP

Path to the input OTU map (i.e., the output from pick_otus.py)

-k SAMPLES_TO_KEEP_FP, --samples_to_keep_fp SAMPLES_TO_KEEP_FP

Path to the file containing Sample IDs to keep in the new OTU map. One Sample ID per line.

-o OUTPUT_OTU_MAP_FP, --output_otu_map_fp OUTPUT_OTU_MAP_FP

Path to the output filtered OTU map

Optional Arguments

-h, --help

Show this help message and exit

-v, --verbose

Specify for verbose description of the script output.