Scroll to navigation



format_input - determine features of organisms, clades, taxonomic units, genes


format_input [-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:

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.
the output file containing the data for LEfSe

optional arguments:

show this help message and exit
the formatted table in txt format
set whether the features are on rows (default) or on columns
set which feature use as class (default 1)
set which feature use as subclass (default -1 meaning no subclass)
set the normalization value (default -1.0 meaning no normalization)
set which feature use as subject (default -1 meaning no subject)
set the policy to adopt with missin values: f removes the features with missing values, s removes samples with missing values (default f)
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)
For biom input files: Set which feature use as class
For biom input files: set which feature use as subclass


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

September 2019 format_input 1.0.8