---
name: "lefse_format_input.py"
section: "1"
platform: "linux"
package: "lefse"
version: "1.1.2-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/lefse_format_input.py"
---

# lefse\_format\_input.py(1)

determine features of organisms, clades, taxonomic units, genes

## 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.