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.