extract_shared_or_unique_otuids.py¶
Parse a BIOM format file and obtain a list of unique OTUIDs found in each category in mapping file.
usage: extract_uniques.py [-h] [-p PREFIX] input_biom_fp output_dir mapping_file category_column
Required arguments¶
-
input_biom_fp
¶
BIOM format file path.
-
mapping_file
¶
Mapping file with category information.
-
category_column
¶
Column in mapping file specifying the category/condition of all samples.
Optional arguments¶
-
-o
OUTPUT_DIR
,
--output_dir
OUTPUT_DIR
¶ Path to save category unique OTUIDs.
-
-p
PREFIX
,
--prefix
PREFIX
¶ Provide specific text to prepend the output file names. By default, the ‘unique’ will be added in front of output filenames.
-
-r
REVERSE
,
--reverse
REVERSE
¶ Get shared OTUIDs among all unique combinations of groups and write out the results to path provided to this option.
-
-h
,
--help
¶
Show the help message and exit