lefse_format_input.py1

positional arguments:

INPUT_FILE

the input file, feature hierarchical level can be specified with | or . and those symbols must not be present for other reasons in the input file.

OUTPUT_FILE

the output file containing the data for LEfSe

optional arguments:

-h, --help

show this help message and exit

--output_table OUTPUT_TABLE

the formatted table in txt format

-f {c,r}

set whether the features are on rows (default) or on columns

-c [1..n_feats]

set which feature use as class (default 1)

-s [1..n_feats]

set which feature use as subclass (default -1 meaning no subclass)

-o float

set the normalization value (default -1.0 meaning no normalization)

-u [1..n_feats]

set which feature use as subject (default -1 meaning no subject)

-m {f,s}

set the policy to adopt with missing values: f removes the features with missing values, s removes samples with missing values (default f)

-n int

set the minimum cardinality of each subclass (subclasses with low cardinalities will be grouped together, if the cardinality is still low, no pairwise comparison will be performed with them)

-biom_c BIOM_CLASS

For biom input files: Set which feature use as class

-biom_s BIOM_SUBCLASS

For biom input files: set which feature use as subclass