From 6a0a3626baad96deb1e8dc7d27fe1fa15e8c5b98 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 3 Oct 2016 19:16:56 +0000
Subject: Fixed problem that caused R/qtl with permutations to not work
 correctly

---
 .../wqflask/marker_regression/marker_regression.py |  5 +++-
 wqflask/wqflask/marker_regression/rqtl_mapping.py  | 35 ++++++++++++----------
 2 files changed, 23 insertions(+), 17 deletions(-)

diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index bb964961..f2a2eb8c 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -166,7 +166,10 @@ class MarkerRegression(object):
             self.model = start_vars['mapmodel_rqtl_geno']
             if start_vars['pair_scan'] == "true":
                 self.pair_scan = True
-            results = rqtl_mapping.run_rqtl_geno(self.vals, self.dataset, self.method, self.model, self.permCheck, self.num_perm, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan)
+            if self.permCheck and self.num_perm > 0:
+                perm_output, self.suggestive, self.significant, results = rqtl_mapping.run_rqtl_geno(self.vals, self.dataset, self.method, self.model, self.permCheck, self.num_perm, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan)
+            else:
+                results = rqtl_mapping.run_rqtl_geno(self.vals, self.dataset, self.method, self.model, self.permCheck, self.num_perm, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan)
         elif self.mapping_method == "reaper":
             if "startMb" in start_vars: #ZS: Check if first time page loaded, so it can default to ON
                 if "additiveCheck" in start_vars:
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index 53ea6053..93bf717c 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -1,4 +1,5 @@
 import rpy2.robjects as ro
+import numpy as np
 
 from base.webqtlConfig import TMPDIR
 from utility import webqtlUtil
@@ -72,9 +73,10 @@ def run_rqtl_geno(vals, dataset, method, model, permCheck, num_perm, do_control,
             else:
                 perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", n_perm = num_perm, model=model, method=method)
 
-            process_rqtl_perm_results(num_perm, perm_data_frame)                                          # Functions that sets the thresholds for the webinterface
-
-        return process_rqtl_results(result_data_frame)
+            perm_output, suggestive, significant = process_rqtl_perm_results(num_perm, perm_data_frame)          # Functions that sets the thresholds for the webinterface
+            return perm_output, suggestive, significant, process_rqtl_results(result_data_frame)
+        else:
+            return process_rqtl_results(result_data_frame)
 
 def geno_to_rqtl_function(dataset):        # TODO: Need to figure out why some genofiles have the wrong format and don't convert properly
 
@@ -161,6 +163,19 @@ def process_pair_scan_results(result):
 
     return pair_scan_results
 
+def process_rqtl_perm_results(num_perm, results):
+    perm_vals = []
+    for line in str(results).split("\n")[1:(num_perm+1)]:
+        #print("R/qtl permutation line:", line.split())
+        perm_vals.append(float(line.split()[1]))
+
+    perm_output = perm_vals
+    suggestive = np.percentile(np.array(perm_vals), 67)
+    significant = np.percentile(np.array(perm_vals), 95)
+    print("SIGNIFICANT:", significant)
+
+    return perm_output, suggestive, significant
+    
 def process_rqtl_results(result):        # TODO: how to make this a one liner and not copy the stuff in a loop
     qtl_results = []
 
@@ -175,16 +190,4 @@ def process_rqtl_results(result):        # TODO: how to make this a one liner an
         marker['lod_score'] = output[i][2]
         qtl_results.append(marker)
 
-    return qtl_results
-
-def process_rqtl_perm_results(num_perm, results):
-    perm_vals = []
-    for line in str(results).split("\n")[1:(num_perm+1)]:
-        #print("R/qtl permutation line:", line.split())
-        perm_vals.append(float(line.split()[1]))
-
-    perm_output = perm_vals
-    suggestive = np.percentile(np.array(perm_vals), 67)
-    significant = np.percentile(np.array(perm_vals), 95)
-
-    return perm_output, suggestive, significant 
\ No newline at end of file
+    return qtl_results 
\ No newline at end of file
-- 
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