[PATCH 050/100] Using out-of-tree storage. Added comments for plink,

 gemma.

3 files changed, 10 insertions, 38 deletions

diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index cfcd4783..ae426621 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -12,8 +12,11 @@ def run_gemma(this_dataset, samples, vals):
 
     gen_pheno_txt_file(this_dataset, samples, vals)
 
-    os.chdir(GEMMA_PATH)
+    # Don't do this!
+    # os.chdir("{}gemma".format(webqtlConfig.HTMLPATH))
 
+    # use GEMMA_RUN in the next one, create a unique temp file
+    
     gemma_command = GEMMA_COMMAND + ' -bfile %s/%s -k %s/output/%s.cXX.txt -lmm 1 -o %s_output' % (GEMMA_PATH,
                                                                                     this_dataset.group.name,
                                                                                     GEMMA_PATH,
@@ -46,4 +49,4 @@ def parse_gemma_output(this_dataset):
                 p_values.append(float(line.split("\t")[10]))
 
     #print("p_values: ", p_values)
-    return included_markers, p_values
\ No newline at end of file
+    return included_markers, p_values
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 1b32b05b..d1c0d9bc 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -30,16 +30,12 @@ from flask import Flask, g
 from base.trait import GeneralTrait
 from base import data_set
 from base import species
-# from base import webqtlConfig
 from utility import webqtlUtil
 from utility import helper_functions
 from utility import Plot, Bunch
 from utility import temp_data
 from utility.benchmark import Bench
 from wqflask.marker_regression import gemma_mapping
-#from wqflask.marker_regression import qtl_reaper_mapping
-#from wqflask.marker_regression import plink_mapping
-#from wqflask.marker_regression import rqtl_mapping
 
 from utility.tools import locate, locate_ignore_error, PYLMM_COMMAND, GEMMA_COMMAND, PLINK_COMMAND
 from utility.external import shell
@@ -297,22 +293,14 @@ class MarkerRegression(object):
         included_markers, p_values = self.parse_gemma_output()
         
         self.dataset.group.get_specified_markers(markers = included_markers)
-        
-        #for marker in self.dataset.group.markers.markers:
-        #    if marker['name'] not in included_markers:
-        #        print("marker:", marker)
-        #        self.dataset.group.markers.markers.remove(marker)
-        #        #del self.dataset.group.markers.markers[marker]
-        
         self.dataset.group.markers.add_pvalues(p_values)
-
         return self.dataset.group.markers.markers
 
-
     def parse_gemma_output(self):
         included_markers = []
         p_values = []
-        with open("/home/zas1024/gene/web/gemma/output/{}_output.assoc.txt".format(self.dataset.group.name)) as output_file:
+        # Use a temporary file name here!
+        with open(webqtlConfig.GENERATED_TEXT_DIR+"/{}_output.assoc.txt".format(self.dataset.group.name)) as output_file:
             for line in output_file:
                 if line.startswith("chr"):
                     continue
@@ -325,31 +313,12 @@ class MarkerRegression(object):
 
     def gen_pheno_txt_file(self):
         """Generates phenotype file for GEMMA"""
-        
-        #with open("/home/zas1024/gene/web/gemma/tmp_pheno/{}.txt".format(filename), "w") as outfile:
-        #    for sample, i in enumerate(self.samples):
-        #        print("sample:" + str(i))
-        #        print("self.vals[i]:" + str(self.vals[sample]))
-        #        outfile.write(str(i) + "\t" + str(self.vals[sample]) + "\n")
-                
-        with open("/home/zas1024/gene/web/gemma/{}.fam".format(self.dataset.group.name), "w") as outfile:
+        with open(webqtlConfig.GENERATED_TEXT_DIR+"{}.fam".format(self.dataset.group.name), "w") as outfile:
             for i, sample in enumerate(self.samples):
                 outfile.write(str(sample) + " " + str(sample) + " 0 0 0 " + str(self.vals[i]) + "\n")
-
-    #def gen_plink_for_gemma(self, filename):
-    #    
-    #    make_bed = "/home/zas1024/plink/plink --file /home/zas1024/plink/%s --noweb --no-fid --no-parents --no-sex --no-pheno --pheno %s%s.txt --out %s%s --make-bed" % (webqtlConfig.HTMLPATH,
-    #                                                                                                                                             webqtlConfig.HTMLPATH,
-    #                                                                                                                                             self.dataset.group.name,
-    #                                                                                                                                             webqtlConfig.TMPDIR,
-    #                                                                                                                                             filename,
-    #                                                                                                                                             webqtlConfig.TMPDIR,
-    #                                                                                                                                             filename)
-    #
-    #
     
     def run_rqtl_plink(self):
-        os.chdir("/home/zas1024/plink")
+        # os.chdir("/home/zas1024/plink") never do this!!
         
         output_filename = webqtlUtil.genRandStr("%s_%s_"%(self.dataset.group.name, self.this_trait.name))
         
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index b35bbbf9..4979d45d 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -458,7 +458,7 @@ def export_pdf():
     svg_xml = request.form.get("data", "Invalid data")
     print("svg_xml:", svg_xml)
     filename = request.form.get("filename", "interval_map_pdf")
-    filepath = "/home/zas1024/gene/wqflask/output/"+filename
+    filepath = GENERATED_IMAGE_DIR+filename
     pdf_file = cairosvg.svg2pdf(bytestring=svg_xml)
     response = Response(pdf_file, mimetype="application/pdf")
     response.headers["Content-Disposition"] = "attachment; filename=%s"%filename