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.