Bug fixes for single replicate with >2 conditions and reading args.txt

Author: kynnemall

superviolin/setup.py

@@ -15,7 +15,7 @@
 setup(
       name = "superviolin",
       py_modules = ["plot_cli", "plot"],      
-      version = "1.0.2",
+      version = "1.0.3",
       url = "",
       description = "Python CLI to make Violin SuperPlots",
       long_description = long_description,

superviolin/superviolin/plot.py

@@ -5,7 +5,6 @@
 @author: Martin Kenny
 """
 
-import os
 import numpy as np
 import pandas as pd
 import scikit_posthocs as sp
@@ -639,7 +638,7 @@ def get_statistics(self, centre_val="mean", paired="no",
 
         num_groups = len(self.subgroups)
 
-        if num_groups > 2:
+        if num_groups > 2 and len(self.unique_reps) > 1:
             # compute one-way ANOVA test results
             stat, p = f_oneway(*data)
 
@@ -669,6 +668,10 @@ def get_statistics(self, centre_val="mean", paired="no",
                 else:
                     print(f"Paired t-test P-value: {p:.3f}")
 
+        else:
+            stat = "Can't run statistics for only 1 replicate"
+            p = stat
+            print(p)
         # plot statistics if only 2 or 3 groups
         if on_plot == "yes" and num_groups in [2, 3]:
             ax = plt.gca()

superviolin/superviolin/plot_cli.py

@@ -38,14 +38,15 @@ def process_txt(txt):
     lines = [i.rstrip() for i in txt if not i.startswith("#")]
     lines = [i for i in lines if len(i) > 0]
     for l in lines:
-        k, v = l.replace("\n", "").split(": ")
-        try:
-            arg_dict[k] = float(v)
-        except ValueError:
-            if k == "None":
-                arg_dict[k] = None
-            else:
-                arg_dict[k] = v
+        if ":" in l:
+            k, v = l.replace("\n", "").split(": ")
+            try:
+                arg_dict[k] = float(v)
+            except ValueError:
+                if k == "None":
+                    arg_dict[k] = None
+                else:
+                    arg_dict[k] = v
     return arg_dict
 
 def get_args(demonstration=False, preferences=False):