Merge pull request #46 from a-slide/dev

Dev
a-slide · Oct 20, 2020 · a4d8312 · a4d8312
2 parents 489f4c0 + 7a1d22f
commit a4d8312
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Showing 4 changed files with 30 additions and 29 deletions.
diff --git a/meta.yaml b/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "0.4.22" %}
+{% set version = "0.4.23" %}
 {% set name = "pycoMeth" %}
 
 package:

diff --git a/pycoMeth/Meth_Comp.py b/pycoMeth/Meth_Comp.py
@@ -356,32 +356,33 @@ def multitest_adjust(self):
                 pvalue_list.append(res["pvalue"])
 
         # Adjust values
-        adj_pvalue_list = multipletests(
-            pvals = pvalue_list,
-            alpha = self.pvalue_threshold,
-            method = self.pvalue_adj_method)[1]
-
-        # add adjusted values to appropriate category
-        for i, adj_pvalue in zip(pvalue_idx, adj_pvalue_list):
-
-            # Fix and categorize p-values
-            if adj_pvalue is np.nan or adj_pvalue is None or adj_pvalue>1 or adj_pvalue<0:
-                adj_pvalue = 1.0
-                comment="Non-significant pvalue"
-
-            elif adj_pvalue <= self.pvalue_threshold:
-                # Correct very low pvalues to minimal float size
-                if adj_pvalue == 0:
-                    adj_pvalue = self.min_pval
-                # update counter if pval is still significant after adjustment
-                comment = "Significant pvalue"
-            else:
-                comment= "Non-significant pvalue"
-
-            # update counters and update comment and adj pavalue
-            self.counter[comment]+=1
-            self.res_list[i]["comment"] = comment
-            self.res_list[i]["adj_pvalue"] = adj_pvalue
+        if pvalue_list:
+            adj_pvalue_list = multipletests(
+                pvals = pvalue_list,
+                alpha = self.pvalue_threshold,
+                method = self.pvalue_adj_method)[1]
+
+            # add adjusted values to appropriate category
+            for i, adj_pvalue in zip(pvalue_idx, adj_pvalue_list):
+
+                # Fix and categorize p-values
+                if adj_pvalue is np.nan or adj_pvalue is None or adj_pvalue>1 or adj_pvalue<0:
+                    adj_pvalue = 1.0
+                    comment="Non-significant pvalue"
+
+                elif adj_pvalue <= self.pvalue_threshold:
+                    # Correct very low pvalues to minimal float size
+                    if adj_pvalue == 0:
+                        adj_pvalue = self.min_pval
+                    # update counter if pval is still significant after adjustment
+                    comment = "Significant pvalue"
+                else:
+                    comment= "Non-significant pvalue"
+
+                # update counters and update comment and adj pavalue
+                self.counter[comment]+=1
+                self.res_list[i]["comment"] = comment
+                self.res_list[i]["adj_pvalue"] = adj_pvalue
 
 #~~~~~~~~~~~~~~~~~~~~~~~~~~~Comp_Writer HELPER CLASS~~~~~~~~~~~~~~~~~~~~~~~~~~~#
 class Comp_Writer():

diff --git a/pycoMeth/__init__.py b/pycoMeth/__init__.py
@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
 
 # Define self package variable
-__version__ = "0.4.22"
+__version__ = "0.4.23"
 __description__ = 'DNA methylation analysis downstream to Nanopolish for Oxford Nanopore DNA sequencing datasets'
diff --git a/setup.py b/setup.py
@@ -5,7 +5,7 @@
 
 # Define package info
 name = "pycoMeth"
-version = "0.4.22"
+version = "0.4.23"
 description = "DNA methylation analysis downstream to Nanopolish for Oxford Nanopore DNA sequencing datasets"
 with open("README.md", "r") as fh:
     long_description = fh.read()