Changed GEMMA mapping to use -lmm 2 (Likelihood ratio test) as a parameter instead of -lmm 1 (Wald test)

Added script to convert .geno files to JSON to maintenance folder (geno_to_json.py)

3 files changed, 19 insertions, 12 deletions

diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 157e4f33..0e31e73e 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -33,7 +33,7 @@ def run_gemma(this_dataset, samples, vals, covariates, method, use_loco):
         gen_covariates_file(this_dataset, covariates)
 
     if method == "gemma_plink":
-        gemma_command = GEMMA_COMMAND + ' -bfile %s/%s -k %s/%s.cXX.txt -lmm 1 -maf 0.1' % (flat_files('mapping'),
+        gemma_command = GEMMA_COMMAND + ' -bfile %s/%s -k %s/%s.cXX.txt -lmm 2 -maf 0.1' % (flat_files('mapping'),
                                                                                         this_dataset.group.name,
                                                                                         flat_files('mapping'),
                                                                                         this_dataset.group.name)
@@ -43,7 +43,7 @@ def run_gemma(this_dataset, samples, vals, covariates, method, use_loco):
                                                                                    webqtlConfig.GENERATED_IMAGE_DIR,
                                                                                    this_dataset.group.name)
         else:
-            #gemma_command = GEMMA_COMMAND + ' -bfile %s/%s -k %s/%s.sXX.txt -lmm 1 -maf 0.1 -o %s_output' % (flat_files('mapping'),
+            #gemma_command = GEMMA_COMMAND + ' -bfile %s/%s -k %s/%s.sXX.txt -lmm 2 -maf 0.1 -o %s_output' % (flat_files('mapping'),
             gemma_command += ' -outdir %s -o %s_output' % (webqtlConfig.GENERATED_IMAGE_DIR,
                                                            this_dataset.group.name)
     else:
@@ -69,20 +69,20 @@ def run_gemma(this_dataset, samples, vals, covariates, method, use_loco):
 
             gwa_output_filename = this_dataset.group.name + "_GWA_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6))
             if covariates != "":
-                gemma_command += ' -c %s/%s_covariates.txt -a %s/%s_snps.txt -lmm 1 -maf 0.1 -debug > %s/gn2/%s.json' % (flat_files('mapping'),
+                gemma_command += ' -c %s/%s_covariates.txt -a %s/%s_snps.txt -lmm 2 -maf 0.1 -debug > %s/gn2/%s.json' % (flat_files('mapping'),
                                                                                                                                          this_dataset.group.name,
                                                                                                                                          flat_files('genotype/bimbam'),
                                                                                                                                          genofile_name,
                                                                                                                                          TEMPDIR,
                                                                                                                                          gwa_output_filename)
             else:
-                gemma_command += ' -a %s/%s_snps.txt -lmm 1 -maf 0.1 -debug > %s/gn2/%s.json' % (flat_files('genotype/bimbam'),
+                gemma_command += ' -a %s/%s_snps.txt -lmm 2 -maf 0.1 -debug > %s/gn2/%s.json' % (flat_files('genotype/bimbam'),
                                                                                                                  genofile_name,
                                                                                                                  TEMPDIR,
                                                                                                                  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'),
+            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 2 -maf 0.1' % (flat_files('genotype/bimbam'),
                                                                                             genofile_name,
                                                                                             flat_files('genotype/bimbam'),
                                                                                             genofile_name,
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index da713325..8e9c5b4c 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -1062,10 +1062,6 @@ class MarkerRegression(object):
 
                 #draw gray blocks for 3' and 5' UTR blocks
                 if cdsStart and cdsEnd:
-                    logger.debug("txStart:", txStart)
-                    logger.debug("cdsStart:", cdsStart)
-                    logger.debug("txEnd:", txEnd)
-                    logger.debug("cdsEnd:", cdsEnd)
                     utrStartPix = (txStart-startMb)*plotXScale + xLeftOffset
                     utrEndPix = (cdsStart-startMb)*plotXScale + xLeftOffset
                     if (utrStartPix < xLeftOffset):
@@ -1721,8 +1717,8 @@ class MarkerRegression(object):
         for i, qtlresult in enumerate(self.qtlresults):
             m = 0
             thisLRSColor = self.colorCollection[0]
-
             if qtlresult['chr'] != previous_chr and self.selectedChr == -1:
+
                 if self.manhattan_plot != True:
                     canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
 
@@ -1760,7 +1756,6 @@ class MarkerRegression(object):
                 AdditiveCoordXY = []
                 previous_chr = qtlresult['chr']
                 previous_chr_as_int += 1
-
                 newStartPosX = (self.ChrLengthDistList[previous_chr_as_int - 1]+self.GraphInterval)*plotXScale
                 if newStartPosX != oldStartPosX:
                     startPosX += newStartPosX
@@ -1773,7 +1768,6 @@ class MarkerRegression(object):
                 this_chr = str(self.ChrList[self.selectedChr][1]+1)
             if self.selectedChr == -1 or str(qtlresult['chr']) == this_chr:
                 Xc = startPosX + (qtlresult['Mb']-startMb)*plotXScale
-
                 # updated by NL 06-18-2011:
                 # fix the over limit LRS graph issue since genotype trait may give infinite LRS;
                 # for any lrs is over than 460(LRS max in this system), it will be reset to 460
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 0ecf1eb9..d40a7bd6 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -343,6 +343,19 @@
                             </div>
                         </div>
                         <div class="mapping_method_fields form-group">
+                            <label style="text-align: right;" class="col-xs-3 control-label">Use LOCO</label>
+                            <div style="margin-left:20px;" class="col-xs-6 controls">
+                                <label class="radio-inline">
+                                    <input type="radio" name="use_loco" value="True" checked="">
+                                    Yes
+                                </label>
+                                <label class="radio-inline">
+                                    <input type="radio" name="use_loco" value="False">
+                                    No
+                               </label>
+                            </div>
+                        </div>
+                        <div class="mapping_method_fields form-group">
                             <label style="text-align: right;" class="col-xs-3 control-label">Covariates</label>
                             <div style="margin-left:20px;" class="col-xs-7">
                               {% if g.user_session.user_ob and (g.user_session.user_ob.display_num_collections() == "") %}