table of contents
| LEFSE_FORMAT_INPUT.PY(1) | User Commands | LEFSE_FORMAT_INPUT.PY(1) |
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.
| September 2021 | lefse_format_input.py 1.1.2 |