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.

usage: pick_otus_condense.py [-h] -s SEQS_OTUS -n NON_UNIQUE_OTU_MATRIX [-o CONDENSED_SEQS_OTUS_FILE] [-v]

Required arguments

-s SEQS_OTUS, --seqs_otus SEQS_OTUS

The list of OTU IDs and their associated sequence IDs.

-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.

-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

-h, --help

Show the help message and exit

-v, --verbose

Print detailed information about script operation.