===================== pick_otus_condense.py ===================== Step 3 of the condensing process. Condense the QIIME pick_otus.py script output by moving the sequences associated with non-unique OTUs to OTU IDs that were identified as unique. .. code-block:: bash usage: pick_otus_condense.py [-h] -s SEQS_OTUS -n NON_UNIQUE_OTU_MATRIX [-o CONDENSED_SEQS_OTUS_FILE] [-v] Required arguments ^^^^^^^^^^^^^^^^^^ .. cmdoption:: -s SEQS_OTUS, --seqs_otus SEQS_OTUS The list of OTU IDs and their associated sequence IDs. .. cmdoption:: -n NON_UNIQUE_OTU_MATRIX, --non_unique_otu_matrix NON_UNIQUE_OTU_MATRIX The list of unique OTU IDs associated with the OTU IDs they replaced. .. cmdoption:: -o CONDENSED_SEQS_OTUS_FILE, --condensed_seqs_otus_file CONDENSED_SEQS_OTUS_FILE The condensed set of OTU IDs and the matching sequences. By default outputs to condensed_seqs_otus.txt Optional arguments ^^^^^^^^^^^^^^^^^^ .. cmdoption:: -h, --help Show the help message and exit .. cmdoption:: -v, --verbose Print detailed information about script operation.