From 753f7da6a468606aa672235c839054e3b913ac83 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 24 Mar 2022 20:00:52 +0000
Subject: Fix qtlreaper results sorting to deal with M as chromosome (should be
 at the end)

Not sure how best to do this; I just had the sort algorithm change "M" to "z" (which will always be sorted last, behind X and Y)
---
 wqflask/wqflask/marker_regression/qtlreaper_mapping.py | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

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)
-- 
cgit v1.2.3


From 1964871492efdb09b0c85861fb4d9018acdfb7e6 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 24 Mar 2022 20:02:59 +0000
Subject: Check if there's only one coordinate for interval mapping

This is meant to deal with edge cases where there's only a single coordinate for a chromosome when doing interval mapping (which causes an error, since interval mapping requires that markers be linked within each chromosome)
---
 wqflask/wqflask/marker_regression/display_mapping_results.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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)
 
-- 
cgit v1.2.3