condense_workflow.py

This workflow script will run all three steps of the OTU condensing pipeline automatically with the default output file settings.

usage: condense_workflow.py [-h] -i ASSIGNED_TAXONOMY_FN -r REP_SET_FN -s SEQS_OTUS_FN [-L {k,p,c,o,f,g,s}] [-v]

Required arguments

-i ASSIGNED_TAXONOMY_FN, --assigned_taxonomy_fn ASSIGNED_TAXONOMY_FN

The taxonomy file output by the assign_taxonomy script.

-r REP_SET_FN, --rep_set_fn REP_SET_FN

The set of representative sequences.

-s SEQS_OTUS_FN, --seqs_otus_fn SEQS_OTUS_FN

The list of OTU IDs and their associated sequence IDs.

Optional arguments

-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.