From 6c0e665d86c501b4a1640e067d46ecb61a3ae1bf Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 22 Sep 2017 16:05:58 +0000
Subject: Fixed issue that caused LOCO to not work when remapping or using
 single chromosome view

---
 wqflask/wqflask/marker_regression/gemma_mapping.py         | 5 +++--
 wqflask/wqflask/marker_regression/marker_regression_gn1.py | 4 ++++
 wqflask/wqflask/templates/marker_regression_gn1.html       | 1 +
 3 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 96a91452..f23c390e 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -70,8 +70,9 @@ def run_gemma(this_dataset, samples, vals, covariates, method, use_loco):
                                                                                                                                          this_dataset.group.name,
                                                                                                                                          gwa_output_filename)
             else:
-                gemma_command += ' -a %s/%s_snps.txt -lmm 1 -maf 0.1 -debug > /home/zas1024/tmp/gn2/GWA.json' % (flat_files('genotype/bimbam'),
-                                                                                                                 this_dataset.group.name)
+                gemma_command += ' -a %s/%s_snps.txt -lmm 1 -maf 0.1 -debug > /home/zas1024/tmp/gn2/%s.json' % (flat_files('genotype/bimbam'),
+                                                                                                                 this_dataset.group.name,
+                                                                                                                 gwa_output_filename)
 
         else:
             gemma_command = GEMMA_COMMAND + ' -g %s/%s_geno.txt -p %s/%s_pheno.txt -a %s/%s_snps.txt -k %s/%s.cXX.txt -lmm 1 -maf 0.1' % (flat_files('genotype/bimbam'),
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 93d75a03..687cfeb5 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -257,6 +257,10 @@ class MarkerRegression(object):
             self.controlLocus = ""
         if 'covariates' in start_vars.keys():
             self.covariates = start_vars['covariates']
+        if 'maf' in start_vars.keys():
+            self.maf = start_vars['maf']
+        if 'use_loco' in start_vars.keys():
+            self.use_loco = start_vars['use_loco']
 
         #try:
         self.selectedChr = int(start_vars['selected_chr'])
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index c6c6bc23..5c457275 100644
--- a/wqflask/wqflask/templates/marker_regression_gn1.html
+++ b/wqflask/wqflask/templates/marker_regression_gn1.html
@@ -20,6 +20,7 @@
         <input type="hidden" name="value:{{ sample }}" value="{{ vals[loop.index - 1] }}">
         {% endfor %}
         <input type="hidden" name="maf">
+        <input type="hidden" name="use_loco" value="{{ use_loco }}">
         <input type="hidden" name="selected_chr" value="{{ selectedChr }}">
         <input type="hidden" name="manhattan_plot" value="{{ manhattan_plot }}">
         <input type="hidden" name="num_perm" value="{{ nperm }}">
-- 
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