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

       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

   positionalarguments:
       INPUT_FILE
              the input file

       OUTPUT_FILE
              the output file containing the data for the visualization module

   optionalarguments:-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
              whether 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)

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