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

       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)

       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

   positionalarguments:
       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

   optionalarguments:-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

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