From d015b37f863c69932072d4ecf9fa1c1cd7fd3ee0 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 8 Feb 2017 18:27:13 +0000
Subject: Changed the way .fam files are written/read, which fixes the issue
 with GEMMA mapping accuracy.

---
 wqflask/maintenance/get_group_samplelists.py       | 2 +-
 wqflask/wqflask/marker_regression/gemma_mapping.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/maintenance/get_group_samplelists.py b/wqflask/maintenance/get_group_samplelists.py
index 2d48ce78..04e94886 100644
--- a/wqflask/maintenance/get_group_samplelists.py
+++ b/wqflask/maintenance/get_group_samplelists.py
@@ -51,6 +51,6 @@ def get_samplelist_from_plink(genofilename):
     samplelist = []
     for line in genofile:
         line = line.split(" ")
-        samplelist.append(line[0])
+        samplelist.append(line[1])
 
     return samplelist
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 66bed5a2..3bde61cd 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -41,7 +41,7 @@ def gen_pheno_txt_file(this_dataset, samples, vals):
                 this_val = -9
             else:
                 this_val = vals[i]
-            outfile.write(line[0] + " " + line[1] + " " + line[2] + " " + line[3] + " " + line[4] + " " + str(this_val) + "\n") 
+            outfile.write("0" + " " + line[1] + " " + line[2] + " " + line[3] + " " + line[4] + " " + str(this_val) + "\n")
 
 def parse_gemma_output(this_dataset):
     included_markers = []
-- 
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