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This filter allows for the removal of sequences and OTUs containing user-specified Sample IDs, for instance, the removal of negative control samples. This script identifies OTUs containing the specified Sample IDs and removes its corresponding sequence from the sequence collection.
Usage: filter_otus_by_sample.py [options]
As a result a new OTU and sequence file is generated and written to a randomly generated folder where the name of the folder starts with “filter_by_otus” Also included in the folder, is another FASTA file containing the removed sequences, leaving the user with 3 files.
The following command can be used, where all options are passed (using the resulting OTU file from pick_otus.py, FASTA file from split_libraries.py and removal of sample ‘PC.636’) with the resulting data being written to the output directory “filtered_otus/”:
filter_otus_by_sample.py -i seqs_otus.txt -f seqs.fna -s PC.636 -o filtered_otus/