transpose_biom.py¶
Transpose a BIOM-format file so that the matrix is sample by species.
usage: transpose_biom.py [-h] -i INPUT_BIOM_FP -m MAPPING [-c MAP_CATEGORY] -o OUTPUT_BIOM_FP [-v]
Required arguments¶
-
-i
INPUT_BIOM_FP
,
--input_biom_fp
INPUT_BIOM_FP
¶ The BIOM-format file.
-
-m
MAPPING
,
--mapping
MAPPING
¶ The mapping file specifying group information for each sample.
-
-o
OUTPUT_BIOM_FP
,
--output_biom_fp
OUTPUT_BIOM_FP
¶ The BIOM-format file to write.
Optional arguments¶
-
-c
MAP_CATEGORY
,
--map_category
MAP_CATEGORY
¶ A mapping category, such as TreatmentType, that will be used to split the data into separate BIOM files; one for each value found in the category.
-
-h
,
--help
¶
Show the help message and exit
-
-v
,
--verbose
¶
Print detailed information about script operation.