Change order of the metrics in the CLI

apcamargo · Jun 2, 2019 · 5ff645d · 5ff645d
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Showing 2 changed files with 5 additions and 6 deletions.
diff --git a/README.md b/README.md
@@ -50,9 +50,9 @@ positional arguments:
   input_file            Expression matrix file in the TSV or CSV formats.
   output_file           Output TSV file containing tissue-specificity values.
   method                Tissue-specificity metric. Allowed values are:
-                        "counts", "tsi", "tau", "gini", "simpson",
-                        "shannon_specificity", "roku_specificity", "zscore",
-                        "spm", "spm_dpm", "js_specificity",
+                        "counts", "tau", "gini", "simpson",
+                        "shannon_specificity", "roku_specificity", "tsi",
+                        "zscore", "spm", "spm_dpm", "js_specificity",
                         "js_specificity_dpm".
 
 optional arguments:

diff --git a/tspex/cli.py b/tspex/cli.py
@@ -39,9 +39,8 @@ def tspex_cli(input_file, output_file, method, log, disable_transformation, thre
 
 
 def main():
-    method_choices = ['counts', 'tsi', 'tau', 'gini', 'simpson', 'shannon_specificity',
-                      'roku_specificity', 'zscore', 'spm', 'spm_dpm', 'js_specificity',
-                      'js_specificity_dpm']
+    method_choices = ['counts', 'tau', 'gini', 'simpson', 'shannon_specificity', 'roku_specificity',
+                      'tsi', 'zscore', 'spm', 'spm_dpm', 'js_specificity', 'js_specificity_dpm']
     parser = argparse.ArgumentParser(
         description='Compute gene tissue-specificity from an expression matrix and save the output.',
         formatter_class=argparse.ArgumentDefaultsHelpFormatter)