Merge pull request #691 from zsloan/bug/fix_qtlreaper_snp_order

Bug/fix qtlreaper snp order

2 files changed, 11 insertions, 2 deletions

diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 920a8d30..034c352b 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -2637,7 +2637,7 @@ class DisplayMappingResults:
                     break
                 m += 1
 
-        if self.manhattan_plot != True:
+        if self.manhattan_plot != True and len(LRSCoordXY) > 1:
             draw_open_polygon(canvas, xy=LRSCoordXY, outline=thisLRSColor,
                               width=lrsEdgeWidth)
 
diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
index 801674e1..c4b495d7 100644
--- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
+++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
@@ -183,7 +183,16 @@ def natural_sort(marker_list):
     Function to naturally sort numbers + strings, adopted from user Mark Byers here: https://stackoverflow.com/questions/4836710/does-python-have-a-built-in-function-for-string-natural-sort
     Changed to return indices instead of values, though, since the same reordering needs to be applied to bootstrap results
     """
-    convert = lambda text: int(text) if text.isdigit() else text.lower()
+
+    def convert(text):
+        if text.isdigit():
+            return int(text)
+        else:
+            if text != "M":
+                return text.lower()
+            else:
+                return "z"
+
     alphanum_key = lambda key: [convert(c) for c in re.split(
         '([0-9]+)', str(marker_list[key]['chr']))]
     return sorted(list(range(len(marker_list))), key=alphanum_key)