pick_otus_condense.py¶
Step 3 of the condensing process. Condense the QIIME pick_otus.py script output by moving the sequences associated with non-unique OTUs to OTU IDs that were identified as unique.
usage: pick_otus_condense.py [-h] -s SEQS_OTUS -n NON_UNIQUE_OTU_MATRIX [-o CONDENSED_SEQS_OTUS_FILE] [-v]
Required arguments¶
-
-s
SEQS_OTUS
,
--seqs_otus
SEQS_OTUS
¶ The list of OTU IDs and their associated sequence IDs.
-
-n
NON_UNIQUE_OTU_MATRIX
,
--non_unique_otu_matrix
NON_UNIQUE_OTU_MATRIX
¶ The list of unique OTU IDs associated with the OTU IDs they replaced.
-
-o
CONDENSED_SEQS_OTUS_FILE
,
--condensed_seqs_otus_file
CONDENSED_SEQS_OTUS_FILE
¶ The condensed set of OTU IDs and the matching sequences. By default outputs to condensed_seqs_otus.txt