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.