biomCtrlFiltering

Giving a list of Sample ID corresponding to control samples, it removes OTU (or feature) from a TSV biom file higher than a given threshold.

Remove OTU by raw abundance:

biomCtrlFiltering.py -i otu_table.tsv -c ctrl_sample_1 -c ctrl_sample_2 -c ... -n 10

Remove OTU by frequency:

biomCtrlFiltering.py -i otu_table.tsv -c ctrl_sample_1 -c ctrl_sample_2 -c ... -f 0.1

Python library:

argparse
csv
logging