Fixed issue with non-LOCO GEMMA mapping

2 files changed, 37 insertions, 58 deletions

diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 895d4ac6..1d9bbb43 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -73,14 +73,6 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf
                                                                                                                gwa_output_filename)
 
       else:
-        #   generate_k_command = GEMMA_COMMAND + ' ' + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/gn2/%s.txt -a %s/%s_snps.txt -gk -outdir %s/gn2/ -o %s' % (flat_files('genotype/bimbam'),
-        #                                                                                   genofile_name,
-        #                                                                                   TEMPDIR,
-        #                                                                                   trait_filename,
-        #                                                                                   flat_files('genotype/bimbam'),
-        #                                                                                   genofile_name,
-        #                                                                                   TEMPDIR,
-        #                                                                                   k_output_filename)
           generate_k_command = GEMMA_WRAPPER_COMMAND + ' --json -- ' + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/gn2/%s.txt -a %s/%s_snps.txt -gk > %s/gn2/%s.json' % (flat_files('genotype/bimbam'),
                                                                                          genofile_name,
                                                                                          TEMPDIR,
@@ -93,31 +85,18 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf
           logger.debug("k_command:" + generate_k_command)
           os.system(generate_k_command)
 
-        #   gemma_command = GEMMA_COMMAND + ' ' + GEMMAOPTS + ' -g %s/%s_geno.txt -p %s/gn2/%s.txt -a %s/%s_snps.txt -k %s/gn2/%s.cXX.txt -lmm 2 -maf %s' % (flat_files('genotype/bimbam'),
-        #                                                                                   genofile_name,
-        #                                                                                   TEMPDIR,
-        #                                                                                   trait_filename,
-        #                                                                                   flat_files('genotype/bimbam'),
-        #                                                                                   genofile_name,
-        #                                                                                   TEMPDIR,
-        #                                                                                   k_output_filename,
-        #                                                                                   maf)
-
-          gemma_command = GEMMA_WRAPPER_COMMAND + ' --json --input %s/gn2/%s.json -- ' % (TEMPDIR, k_output_filename) + GEMMAOPTS + ' -lmm 2 -g %s/%s_geno.txt -p %s/gn2/%s.txt' % (flat_files('genotype/bimbam'),
+          gemma_command = GEMMA_WRAPPER_COMMAND + ' --json --input %s/gn2/%s.json -- ' % (TEMPDIR, k_output_filename) + GEMMAOPTS + ' -a %s/%s_snps.txt -lmm 2 -g %s/%s_geno.txt -p %s/gn2/%s.txt' % (flat_files('genotype/bimbam'),
+                                                                                         genofile_name,
+                                                                                         flat_files('genotype/bimbam'),
                                                                                          genofile_name,
                                                                                          TEMPDIR,
                                                                                          trait_filename)
 
 
           if covariates != "":
-              gemma_command += ' -c %s/%s_covariates.txt' % (flat_files('mapping'), this_dataset.group.name)
-            #   gemma_command += ' -c %s/%s_covariates.txt -outdir %s -o %s_output' % (flat_files('mapping'),
-            #                                                                                                this_dataset.group.name,
-            #                                                                                                webqtlConfig.GENERATED_IMAGE_DIR,
-            #                                                                                                genofile_name)
-        #   else:
-        #       gemma_command += ' -outdir %s -o %s_output' % (webqtlConfig.GENERATED_IMAGE_DIR,
-        #                                                             genofile_name)
+              gemma_command += ' -c %s/%s_covariates.txt > %s/gn2/%s.json' % (flat_files('mapping'), this_dataset.group.name, TEMPDIR, gwa_output_filename)
+          else:
+              gemma_command += ' > %s/gn2/%s.json' % (TEMPDIR, gwa_output_filename)
 
 
       logger.debug("gemma_command:" + gemma_command)
@@ -127,7 +106,7 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf
         marker_obs = parse_loco_output(this_dataset, gwa_output_filename)
         return marker_obs, gwa_output_filename
     else:
-        marker_obs = parse_gemma_output(genofile_name)
+        marker_obs = parse_loco_output(this_dataset, gwa_output_filename)
         return marker_obs
 
 def gen_pheno_txt_file(this_dataset, genofile_name, vals, trait_filename):
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index aa64a910..fbcaefc1 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -671,36 +671,36 @@ def mapping_results_page():
         if template_vars.no_results:
             rendered_template = render_template("mapping_error.html")
         else:
-          #if template_vars.mapping_method != "gemma" and template_vars.mapping_method != "plink":
-          template_vars.js_data = json.dumps(template_vars.js_data,
-                                                 default=json_default_handler,
-                                                 indent="   ")
-
-          result = template_vars.__dict__
-
-          if result['pair_scan']:
-              with Bench("Rendering template"):
-                  img_path = result['pair_scan_filename']
-                  logger.info("img_path:", img_path)
-                  initial_start_vars = request.form
-                  logger.info("initial_start_vars:", initial_start_vars)
-                  imgfile = open(TEMPDIR + img_path, 'rb')
-                  imgdata = imgfile.read()
-                  imgB64 = imgdata.encode("base64")
-                  bytesarray = array.array('B', imgB64)
-                  result['pair_scan_array'] = bytesarray
-                  rendered_template = render_template("pair_scan_results.html", **result)
-          else:
-              gn1_template_vars = display_mapping_results.DisplayMappingResults(result).__dict__
-              #pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL)
-              #logger.info("pickled result length:", len(pickled_result))
-              #Redis.set(key, pickled_result)
-              #Redis.expire(key, 1*60)
-
-              with Bench("Rendering template"):
-                  if (gn1_template_vars['mapping_method'] == "gemma") or (gn1_template_vars['mapping_method'] == "plink"):
-                      gn1_template_vars.pop('qtlresults', None)
-                  rendered_template = render_template("mapping_results.html", **gn1_template_vars)
+            #if template_vars.mapping_method != "gemma" and template_vars.mapping_method != "plink":
+            template_vars.js_data = json.dumps(template_vars.js_data,
+                                                    default=json_default_handler,
+                                                    indent="   ")
+
+            result = template_vars.__dict__
+
+            if result['pair_scan']:
+                with Bench("Rendering template"):
+                    img_path = result['pair_scan_filename']
+                    logger.info("img_path:", img_path)
+                    initial_start_vars = request.form
+                    logger.info("initial_start_vars:", initial_start_vars)
+                    imgfile = open(TEMPDIR + img_path, 'rb')
+                    imgdata = imgfile.read()
+                    imgB64 = imgdata.encode("base64")
+                    bytesarray = array.array('B', imgB64)
+                    result['pair_scan_array'] = bytesarray
+                    rendered_template = render_template("pair_scan_results.html", **result)
+            else:
+                gn1_template_vars = display_mapping_results.DisplayMappingResults(result).__dict__
+                #pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL)
+                #logger.info("pickled result length:", len(pickled_result))
+                #Redis.set(key, pickled_result)
+                #Redis.expire(key, 1*60)
+
+                with Bench("Rendering template"):
+                    if (gn1_template_vars['mapping_method'] == "gemma") or (gn1_template_vars['mapping_method'] == "plink"):
+                        gn1_template_vars.pop('qtlresults', None)
+                    rendered_template = render_template("mapping_results.html", **gn1_template_vars)
 
     return rendered_template