NAME

       lefse_format_input.py - determine features of organisms, clades, taxonomic units, genes

DESCRIPTION

       usage: lefse_format_input.py [-h] [--output_table OUTPUT_TABLE] [-f {c,r}]

       [-c [1..n_feats]] [-s [1..n_feats]] [-o float]
              [-u  [1..n_feats]]  [-m  {f,s}]  [-n  int] [-biom_c BIOM_CLASS] [-biom_s BIOM_SUBCLASS] INPUT_FILE
              OUTPUT_FILE

       LEfSe formatting modules

   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

AUTHOR

       This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage
       of the program.

lefse_format_input.py 1.1.2                      September 2021                         LEFSE_FORMAT_INPUT.PY(1)