otu_condense.py

Step 1 of the condensing process. Take a taxonomy table from the assign_taxonomy QIIME script and prune all redundant taxonomy strings

usage: otu_condense.py [-h] -i INPUT_ASSIGNED_TAXONOMY [-p PRUNED_OUTPUT_FILE] [-n NON_UNIQUE_OUTPUT_FILE] [-l {k,p,c,o,f,g,s}] [-v]

Required arguments

-i INPUT_ASSIGNED_TAXONOMY, --input_assigned_taxonomy INPUT_ASSIGNED_TAXONOMY

The taxonomy file output by the assign_taxonomy script.

Optional arguments

-p PRUNED_OUTPUT_FILE, --pruned_output_file PRUNED_OUTPUT_FILE

The output file for the pruned taxonomy list. Defaults to condensed_assigned_taxonomy.txt

-n NON_UNIQUE_OUTPUT_FILE, --non_unique_output_file NON_UNIQUE_OUTPUT_FILE

The file will contain a list of pruned OTU IDs associated with the OTU IDs they replaced. Defaults to nonunique_otu_matrix.txt

-l {k,p,c,o,f,g,s}, --phylogenetic_level {k,p,c,o,f,g,s}

Set the phylogenetic level at which to define OTUs for condensing and downstream processing. Defaults to species level.

-h, --help

Show the help message and exit

-v, --verbose

Print detailed information about script operation.