NAME

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

DESCRIPTION

       usage: lefse_run.py [-h] [-o str] [-a float] [-w float] [-l float]

       [--nlogs int] [--verbose int] [--wilc int] [-r str]
              [--svm_norm  int]  [-b  int]  [-e int] [-c int] [-f float] [-s {0,1,2}] [--min_c int] [-t str] [-y
              {0,1}] INPUT_FILE OUTPUT_FILE

       LEfSe 1.1.01

   positional arguments:
       INPUT_FILE
              the input file

       OUTPUT_FILE
              the output file containing the data for the visualization module

   optional arguments:
       -h, --help
              show this help message and exit

       -o str set the file for exporting the result (only concise textual form)

       -a float
              set the alpha value for the Anova test (default 0.05)

       -w float
              set the alpha value for the Wilcoxon test (default 0.05)

       -l float
              set the threshold on the absolute value of the logarithmic LDA score (default 2.0)

       --nlogs int
              max log ingluence of LDA coeff

       --verbose int
              verbose execution (default 0)

       --wilc int
              wheter to perform the Wicoxon step (default 1)

       -r str select LDA or SVM for effect size (default LDA)

       --svm_norm int
              whether to normalize the data in [0,1] for SVM feature waiting (default 1 strongly suggested)

       -b int set the number of bootstrap iteration for LDA (default 30)

       -e int set whether perform the wilcoxon test only among the subclasses with the same name (default 0)

       -c int set whether perform the wilcoxon test ing the Curtis's approach [BETA VERSION] (default 0)

       -f float
              set the subsampling fraction value for each bootstrap iteration (default 0.66666)

       -s {0,1,2}
              set the multiple testing correction options. 0 no correction (more strict, default), 1  correction
              for independent comparisons, 2 correction for dependent comparison

       --min_c int
              minimum number of samples per subclass for performing wilcoxon test (default 10)

       -t str set the title of the analysis (default input file without extension)

       -y {0,1}
              (for  multiclass tasks) set whether the test is performed in a one-against-one ( 1 - more strict!)
              or in a one-againstall setting ( 0 - less strict) (default 0)

AUTHOR

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

lefse_run.py 1.1.2                               September 2021                                  LEFSE_RUN.PY(1)