prune_otus.py¶
Parse the OTU-sequence data in two steps. First remove any OTUs that occur in less than a user-defined percent of samples (default 5%). Second, remove any OTUs that make up less than a user-defined percentage of the overall sequences (default 0.01%)
usage: prune_otus.py [-h] -i SEQS_OTUS_FN -t ID_TO_TAXONOMY_FN [-p PERCENT_OF_SAMPLES] [-s PERCENT_OF_SEQUENCES] [-l {k,p,c,o,f,g,s}] [-o OUTPUT_PRUNED_OTUS_FN] [--output_removed_otus_fn OUTPUT_REMOVED_OTUS_FN] [-v]
Required arguments¶
-
-i
SEQS_OTUS_FN
,
--seqs_otus_fn
SEQS_OTUS_FN
¶ The output from the pick OTUs step, e.g. seqs_otus.txt
-
-t
ID_TO_TAXONOMY_FN
,
--id_to_taxonomy_fn
ID_TO_TAXONOMY_FN
¶ Path to tab-delimited file mapping sequences to assigned taxonomy.
Optional arguments¶
-
-p
PERCENT_OF_SAMPLES
,
--percent_of_samples
PERCENT_OF_SAMPLES
¶ OTUs that occur in less than this percent of samples will be removed. Default is 5 percent.
-
-s
PERCENT_OF_SEQUENCES
,
--percent_of_sequences
PERCENT_OF_SEQUENCES
¶ OTUs that occur in less than this percent of total sequences will be removed. Default is 0.01 percent.
-
-l
{k,p,c,o,f,g,s}
,
--phylogenetic_level
{k,p,c,o,f,g,s}
¶ Set the phylogenetic level at which to join OTUs for consideration in pruning. Default is ‘g’(group).
-
-o
OUTPUT_PRUNED_OTUS_FN
,
--output_pruned_otus_fn
OUTPUT_PRUNED_OTUS_FN
¶ The main output file that will contain the remaining OTUs and sequence IDs.
-
--output_removed_otus_fn
OUTPUT_REMOVED_OTUS_FN
¶ The file to write out the set of OTUs that were removed by the filter.
-
-h
,
--help
¶
Show the help message and exit
-
-v
,
--verbose
¶
Print detailed information about script operation.