Merge branch 'master' of https://github.com/genenetwork/genenetwork2

10 files changed, 116 insertions, 26 deletions

diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index b1ab780c..997b692d 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -1,6 +1,9 @@
 import os
 
 from base import webqtlConfig
+from utility.tools import gemma_command
+
+GEMMA_PATH,GEMMA_COMMAND = gemma_command()
 
 def run_gemma(this_dataset, samples, vals): 
     """Generates p-values for each marker using GEMMA"""
@@ -9,9 +12,11 @@ def run_gemma(this_dataset, samples, vals):
 
     gen_pheno_txt_file(this_dataset, samples, vals)
 
-    os.chdir("{}gemma".format(webqtlConfig.HTMLPATH))
+    os.chdir(GEMMA_PATH)
 
-    gemma_command = './gemma -bfile %s -k output_%s.cXX.txt -lmm 1 -o output/%s_output' % (this_dataset.group.name,
+    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,
                                                                                     this_dataset.group.name,
                                                                                     this_dataset.group.name)
     print("gemma_command:" + gemma_command)
@@ -25,14 +30,14 @@ def run_gemma(this_dataset, samples, vals):
 def gen_pheno_txt_file(this_dataset, samples, vals):
     """Generates phenotype file for GEMMA"""
                 
-    with open("{}gemma/{}.fam".format(webqtlConfig.HTMLPATH, this_dataset.group.name), "w") as outfile:
+    with open("{}/{}.fam".format(GEMMA_PATH, this_dataset.group.name), "w") as outfile:
         for i, sample in enumerate(samples):
             outfile.write(str(sample) + " " + str(sample) + " 0 0 0 " + str(vals[i]) + "\n")
 
 def parse_gemma_output(this_dataset):
     included_markers = []
     p_values = []
-    with open("{}gemma/output/{}_output.assoc.txt".format(webqtlConfig.HTMLPATH, this_dataset.group.name)) as output_file:
+    with open("{}/output/{}_output.assoc.txt".format(GEMMA_PATH, this_dataset.group.name)) as output_file:
         for line in output_file:
             if line.startswith("chr"):
                 continue
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index c16c885e..a6fa5274 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -39,10 +39,11 @@ from utility import helper_functions
 from utility import Plot, Bunch
 from utility import temp_data
 from utility.benchmark import Bench
-from utility.tools import pylmm_command, plink_command
+from utility.tools import pylmm_command, plink_command, gemma_command
 
 PYLMM_PATH,PYLMM_COMMAND = pylmm_command()
 PLINK_PATH,PLINK_COMMAND = plink_command()
+GEMMA_PATH,GEMMA_COMMAND = gemma_command()
 
 class MarkerRegression(object):
 
@@ -219,9 +220,9 @@ class MarkerRegression(object):
         
         self.gen_pheno_txt_file()
 
-        os.chdir("/home/zas1024/gene/web/gemma")
+        #os.chdir("/home/zas1024/gene/web/gemma")
 
-        gemma_command = './gemma -bfile %s -k output_%s.cXX.txt -lmm 1 -o %s_output' % (
+        gemma_command = GEMMA_COMMAND + ' -bfile %s -k output_%s.cXX.txt -lmm 1 -o %s_output' % (
                                                                                                  self.dataset.group.name,
                                                                                                  self.dataset.group.name,
                                                                                                  self.dataset.group.name)
@@ -491,7 +492,7 @@ class MarkerRegression(object):
         
         self.gen_pheno_txt_file_plink(pheno_filename = plink_output_filename)
         
-        plink_command = PLINK_COMMAND + ' --noweb --ped %s/%s.ped --no-fid --no-parents --no-sex --no-pheno --map %s/%s.map --pheno %s%s.txt --pheno-name %s --maf %s --missing-phenotype -9999 --out %s%s --assoc ' % (PLINK_PATH, self.dataset.group.name, PLINK_PATH, self.dataset.group.name, webqtlConfig.TMPDIR, plink_output_filename, self.this_trait.name, self.maf, webqtlConfig.TMPDIR, plink_output_filename)
+        plink_command = PLINK_COMMAND + ' --noweb --bed %s/%s.bed --bim %s/%s.bim --fam %s/%s.fam --no-fid --no-parents --no-sex --no-pheno --pheno %s%s.txt --pheno-name %s --maf %s --missing-phenotype -9999 --out %s%s --assoc ' % (PLINK_PATH, self.dataset.group.name, PLINK_PATH, self.dataset.group.name, PLINK_PATH, self.dataset.group.name, webqtlConfig.TMPDIR, plink_output_filename, self.this_trait.name, self.maf, webqtlConfig.TMPDIR, plink_output_filename)
         print("plink_command:", plink_command)        
 
         os.system(plink_command)
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index aa6f9562..d6c48a12 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -161,7 +161,6 @@ class ShowTrait(object):
         def check_plink_gemma():
             if (os.path.isfile(PLINK_PATH+"/"+self.dataset.group.name+".bed") and
                 os.path.isfile(PLINK_PATH+"/"+self.dataset.group.name+".map")):
-
                 return True
             else:
                 return False
diff --git a/wqflask/wqflask/templates/collections/list.html b/wqflask/wqflask/templates/collections/list.html
index 52106eae..0e7612aa 100755
--- a/wqflask/wqflask/templates/collections/list.html
+++ b/wqflask/wqflask/templates/collections/list.html
@@ -4,6 +4,7 @@
     <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
     <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
     <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />
+    <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.bootstrap.css" />
 {% endblock %}
 {% block content %}
 <!-- Start of body -->
@@ -55,6 +56,10 @@
 {% block js %}
     <script type="text/javascript" src="/static/packages/smart-time-ago/lib/timeago.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
+    <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/dataTables.buttons.min.js"></script>
+    <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/buttons.html5.min.js"></script>
+    <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/buttons.bootstrap.min.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colResize.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colReorder.js"></script>
@@ -62,7 +67,15 @@
     <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script>
     <script>
             $('#trait_table').dataTable( {
-                "sDom": "RZtir",
+                "buttons": [
+                    {
+                       extend: 'csvHtml5',
+                       text: 'Download CSV',
+                       title: 'collection_list',
+                       fieldBoundary: '"'
+                    }
+                ],
+                "sDom": "RZBtir",
                 "iDisplayLength": -1,
                 "autoWidth": true,
                 "bDeferRender": true,
diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index 5450f903..a53759c4 100755
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -4,6 +4,7 @@
     <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
     <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
     <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />
+    <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.bootstrap.css" />
 {% endblock %}
 {% block content %}
 <!-- Start of body -->
@@ -73,12 +74,12 @@
             <button class="btn btn-default" id="invert"><span class="glyphicon glyphicon-resize-vertical"></span> Invert</button>
             <button class="btn" id="add" disabled="disabled"><i class="icon-plus-sign"></i> Add Record to Other Collection</button>
             <button class="btn" id="remove" disabled="disabled"><i class="icon-minus-sign"></i> Remove Record</button>
-            <button class="btn btn-primary pull-right"><i class="icon-download icon-white"></i> Download Table</button>
             <br />
             <br />
         <table class="table table-hover table-striped" id='trait_table'>
             <thead>
                 <tr>
+                    <th></th>
                     <th>Index</th>
                     <th>Record</th>
                     <th>Description</th>
@@ -93,10 +94,11 @@
             <tbody>
                 {% for this_trait in trait_obs %}
                 <TR id="trait:{{ this_trait.name }}:{{ this_trait.dataset.name }}">
-                    <TD>{{ loop.index }}
+                    <TD>
                         <INPUT TYPE="checkbox" NAME="searchResult" class="checkbox trait_checkbox"
                                VALUE="{{ data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset.name)) }}">
                     </TD>
+                    <TD>{{ loop.index }}</TD>
                     <TD>
                         <a href="{{ url_for('show_trait_page',
                                 trait_id = this_trait.name,
@@ -129,6 +131,10 @@
 {% block js %}
     <script type="text/javascript" src="/static/new/javascript/search_results.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
+    <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/dataTables.buttons.min.js"></script>
+    <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/buttons.html5.min.js"></script>
+    <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/buttons.bootstrap.min.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colResize.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colReorder.js"></script>
@@ -150,6 +156,7 @@
                 "columns": [
                     { "type": "natural" },
                     { "type": "natural" },
+                    { "type": "natural" },
                     { "type": "natural",
                       "width": "35%"  },
                     { "type": "natural",
@@ -161,7 +168,18 @@
                       "width": "15%"  },
                     { "type": "natural" }
                 ],
-                "sDom": "ZRtir",
+                "buttons": [
+                    {
+                       extend: 'csvHtml5',
+                       text: 'Download CSV',
+                       title: 'collection',
+                       fieldBoundary: '"',
+                       exportOptions: {
+                           columns: [1, 2, 3, 4, 5, 6, 7, 8]
+                       }
+                    }
+                ],
+                "sDom": "ZRBtir",
                 "iDisplayLength": -1,
                 "autoWidth": true,
                 "bDeferRender": true,
diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html
index 0a1839a1..7cc9a1bd 100755
--- a/wqflask/wqflask/templates/gsearch_gene.html
+++ b/wqflask/wqflask/templates/gsearch_gene.html
@@ -6,6 +6,7 @@
     <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/dataTables.fixedHeader.css" >
     <link rel="stylesheet" type="text/css" href="//cdn.datatables.net/fixedcolumns/3.0.4/css/dataTables.fixedColumns.css">
+    <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.bootstrap.css" />
 {% endblock %}
 {% block content %}
 <!-- Start of body -->
@@ -20,7 +21,6 @@
             <button class="btn btn-default" id="deselect_all"><span class="glyphicon glyphicon-remove"></span> Deselect All</button>
             <button class="btn btn-default" id="invert"><span class="glyphicon glyphicon-resize-vertical"></span> Invert</button>
             <button class="btn btn-default" id="add" disabled ><span class="glyphicon glyphicon-plus-sign"></span> Add</button>
-            <button class="btn btn-primary pull-right"><span class="glyphicon glyphicon-download"></span> Download Table</button>
             <input type="text" id="searchbox" class="form-control" style="width: 180px; display: inline;" placeholder="Search This Table For ...">
             <input type="text" id="select_top" class="form-control" style="width: 120px; display: inline;" placeholder="Select Top ...">
 
@@ -77,6 +77,10 @@
     <script language="javascript" type="text/javascript" src="/static/new/javascript/search_results.js"></script>
     
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
+    <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/dataTables.buttons.min.js"></script>
+    <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/buttons.html5.min.js"></script>
+    <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/buttons.bootstrap.min.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colReorder.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colResize.js"></script>
@@ -169,7 +173,18 @@
                     { "type": "cust-txt" }
                 ],
                 "order": [[ 1, "asc" ]],
-                "sDom": "RZtir",
+                "buttons": [
+                    {
+                       extend: 'csvHtml5',
+                       text: 'Download CSV',
+                       title: 'search_results',
+                       fieldBoundary: '"',
+                       exportOptions: {
+                           columns: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13]
+                       }
+                    }
+                ],
+                "sDom": "RZBtir",
                 "autoWidth": false,
                 "bLengthChange": true,
                 "bDeferRender": true,
diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html
index 2527bebf..0bdc4f4e 100755
--- a/wqflask/wqflask/templates/gsearch_pheno.html
+++ b/wqflask/wqflask/templates/gsearch_pheno.html
@@ -4,6 +4,7 @@
     <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
     <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
     <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />
+    <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.bootstrap.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/dataTables.fixedHeader.css" >
     <link rel="stylesheet" type="text/css" href="//cdn.datatables.net/fixedcolumns/3.0.4/css/dataTables.fixedColumns.css">
 {% endblock %}
@@ -20,7 +21,6 @@
             <button class="btn btn-default" id="deselect_all"><span class="glyphicon glyphicon-remove"></span> Deselect All</button>
             <button class="btn btn-default" id="invert"><span class="glyphicon glyphicon-resize-vertical"></span> Invert</button>
             <button class="btn btn-default" id="add" disabled ><span class="glyphicon glyphicon-plus-sign"></span> Add</button>
-            <button class="btn btn-primary pull-right"><span class="glyphicon glyphicon-download"></span> Download Table</button>
             <input type="text" id="searchbox" class="form-control" style="width: 200px; display: inline;" placeholder="Search This Table For ...">
             <input type="text" id="select_top" class="form-control" style="width: 200px; display: inline;" placeholder="Select Top ...">
             <br />
@@ -70,6 +70,10 @@
     <script language="javascript" type="text/javascript" src="/static/new/javascript/search_results.js"></script>
     
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
+    <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/dataTables.buttons.min.js"></script>
+    <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/buttons.html5.min.js"></script>
+    <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/buttons.bootstrap.min.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/js_external/jszip.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colReorder.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colResize.js"></script>
@@ -137,7 +141,18 @@
                     { "type": "natural" }
                 ],
                 "order": [[ 1, "asc" ]],
-                "sDom": "RZtir",
+                "buttons": [
+                    {
+                       extend: 'csvHtml5',
+                       text: 'Download CSV',
+                       title: 'search_results',
+                       fieldBoundary: '"',
+                       exportOptions: {
+                           columns: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
+                       }
+                    }
+                ],
+                "sDom": "RZBtir",
                 "autoWidth": false,
                 "bLengthChange": true,
                 "bDeferRender": true,
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 02365b1d..ff3e04bb 100755
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -167,7 +167,7 @@
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colResize.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colReorder.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.fixedHeader.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.fixedHeader.min.js"></script>
     <script language="javascript" type="text/javascript" src="//cdn.datatables.net/fixedcolumns/3.0.4/js/dataTables.fixedColumns.min.js"></script>
 	
     <script type="text/javascript" charset="utf-8">
@@ -234,7 +234,15 @@
                 ],
                 "order": [[1, "asc" ]],
                 "buttons": [
-                    'csv'
+                    {
+                       extend: 'csvHtml5',
+                       text: 'Download CSV',
+                       title: 'search_results',
+                       fieldBoundary: '"',
+                       exportOptions: {
+                           columns: [1, 2, 3, 4, 5, 6, 7, 8, 9]
+                       }
+                    }
                 ],
                 "sDom": "RZBtir",
                 "iDisplayLength": -1,
@@ -260,7 +268,15 @@
                 ],
                 "order": [[1, "asc" ]],
                 "buttons": [
-                    'csv'
+                    {
+                       extend: 'csvHtml5',
+                       text: 'Download CSV',
+                       title: 'search_results',
+                       fieldBoundary: '"',
+                       exportOptions: {
+                           columns: [1, 2, 3, 4, 5, 6, 7]
+                       }
+                    }
                 ],
                 "sDom": "RZBtir",
                 "iDisplayLength": -1,
@@ -281,7 +297,15 @@
                 ],
                 "order": [[1, "asc" ]],
                 "buttons": [
-                    'csv'
+                    {
+                       extend: 'csvHtml5',
+                       text: 'Download CSV',
+                       title: 'search_results',
+                       fieldBoundary: '"',
+                       exportOptions: {
+                           columns: [1, 2, 3]
+                       }
+                    }
                 ],
                 "sDom": "RZBtir",
                 "iDisplayLength": -1,
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index c23cb010..6252f6f4 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -256,8 +256,8 @@
                 <div class="tab-pane" id="plink">
                     <div style="padding: 20px" class="form-horizontal">
                         <div class="mapping_method_fields form-group">
-                            <label for="maf_plink" class="col-xs-2 control-label">Minor allele threshold</label>
-                            <div style="margin-left: 20px;" class="col-xs-2 controls">
+                            <label for="maf_plink" class="col-xs-3 control-label">Minor allele threshold</label>
+                            <div style="margin-left: 20px;" class="col-xs-3 controls">
                                 <input name="maf_plink" value="0.01" type="text" class="form-control">
                             </div>
                         </div>
@@ -276,8 +276,8 @@
                 <div class="tab-pane" id="gemma">
                     <div style="padding: 20px" class="form-horizontal">
                         <div class="mapping_method_fields form-group">
-                            <label for="maf_gemma" class="col-xs-2 control-label">Minor allele threshold</label>
-                            <div style="margin-left: 20px;" class="col-xs-2 controls">
+                            <label for="maf_gemma" class="col-xs-3 control-label">Minor allele threshold</label>
+                            <div style="margin-left: 20px;" class="col-xs-3 controls">
                                 <input name="maf_gemma" value="0.01" type="text" class="form-control">
                             </div>
                         </div>
diff --git a/wqflask/wqflask/wgcna/wgcna_analysis.py b/wqflask/wqflask/wgcna/wgcna_analysis.py
index f23b1417..9e9f41bc 100644
--- a/wqflask/wqflask/wgcna/wgcna_analysis.py
+++ b/wqflask/wqflask/wgcna/wgcna_analysis.py
@@ -86,8 +86,8 @@ class WGCNA(object):
             trait = t[0]                  # R uses vectors every single element is a vector
             for s in uStrainsR:
                 strain = s[0]             # R uses vectors every single element is a vector
-                rM.rx[strain, trait] = self.input[trait].get(strain)  # Update the matrix location
                 #DEBUG: print(trait, strain, " in python: ", self.input[trait].get(strain), "in R:", rM.rx(strain,trait)[0])
+                rM.rx[strain, trait] = self.input[trait].get(strain)  # Update the matrix location
                 sys.stdout.flush()
 
         self.results = {}