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authorzsloan2016-03-01 21:01:55 +0000
committerzsloan2016-03-01 21:01:55 +0000
commitfa6aff6719cf180d4a5941d3ee6a538b33230124 (patch)
tree125bee1fd19f53643209cfc693e1c4e2d8cb283d /wqflask
parentc5ae746a29125bddeda5609916cf9ec25152cc35 (diff)
parentd38f4c6c2176d935bcb4f235fb4eee8b3ad703c2 (diff)
downloadgenenetwork2-fa6aff6719cf180d4a5941d3ee6a538b33230124.tar.gz
Merge branch 'master' of https://github.com/genenetwork/genenetwork2
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/wqflask/marker_regression/gemma_mapping.py13
-rwxr-xr-xwqflask/wqflask/marker_regression/marker_regression.py9
-rwxr-xr-xwqflask/wqflask/show_trait/show_trait.py1
-rwxr-xr-xwqflask/wqflask/templates/collections/list.html15
-rwxr-xr-xwqflask/wqflask/templates/collections/view.html24
-rwxr-xr-xwqflask/wqflask/templates/gsearch_gene.html19
-rwxr-xr-xwqflask/wqflask/templates/gsearch_pheno.html19
-rwxr-xr-xwqflask/wqflask/templates/search_result_page.html32
-rwxr-xr-xwqflask/wqflask/templates/show_trait_mapping_tools.html8
-rw-r--r--wqflask/wqflask/wgcna/wgcna_analysis.py2
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 = {}