From baff5eb1e890a4a8b33fb1917a1c17d3b1737959 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 26 Jun 2015 18:29:49 +0000
Subject: Fixed bug where mapping results sometimes wouldn't display. This
 would occur due to a chromosome (in this case the last) not having any
 markers.

Improved the way plink gets its path/command to use a method similar to the
one Pjotr used with pylmm. I'll also do this for the other mapping methods.

Fixed issue where the Y axis would always say LOD score. It now says LRS for
mapping methods that return LRS

Switched interval mapping (qtl reaper) to use the marker_regression template and removed the interval_mapping template (since it's unnecessary)

Some commented out changes remain (in show_trait_mapping_tools and create_lodchart) from when I was attempting to open the mapping results
in a new page. I had resolved every issue but the mapping javascript (lod_chart) not
being able to access js_data (which has all the result data; markers, p-values, etc). I'm pretty
sure that this is because js_data was inserted into the html after the page was loaded while
the chart code ran immediately. I experimented with adding a short timeout to the mapping
javascript and data table javascript, but while it worked for the table it did not work for the
mapping figure. I don't know why this is.
---
 wqflask/utility/tools.py | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

(limited to 'wqflask/utility')

diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 1a5c19d9..6e35f00a 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -49,3 +49,21 @@ def pylmm_command(default=None):
     path = get_setting('PYLMM_PATH',default,guess,get_valid_path)
     pylmm_command = 'python '+path+'/pylmm_gn2/lmm.py'
     return path,pylmm_command
+
+def plink_command(default=None):
+    """
+    Return the path to the repository and the python command to call
+    """
+    def get_valid_path(path):
+        """Test for a valid repository"""
+        if path:
+            sys.stderr.write("Trying PLINK_PATH in "+path+"\n")
+        if path and os.path.isfile(path+'/plink'):
+            return path
+        else:
+            None
+
+    guess = os.environ.get('HOME')+'/plink'
+    path = get_setting('PLINK_PATH',default,guess,get_valid_path)
+    plink_command = path+'/plink'
+    return path,plink_command
\ No newline at end of file
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