Got non-LOCO GEMMA mapping working with gemma-wrapper (so caching should work for that now)

Fixed position digits and row highlighting on interval analyst table

Updated default MAF to 0.05

Updated footer text

6 files changed, 74 insertions, 63 deletions

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 4fee5c7a..d766e284 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -433,7 +433,7 @@ def datasets(group_name, this_group = None):
             and InbredSet.Name like %s
             and ProbeSetFreeze.public > %s
             and ProbeSetFreeze.confidentiality < 1
-          ORDER BY Tissue.Name)
+          ORDER BY Tissue.Name, ProbeSetFreeze.OrderList DESC)
         ''' % (group_name, webqtlConfig.PUBLICTHRESH,
               group_name, webqtlConfig.PUBLICTHRESH,
               "'" + group_name + "'", webqtlConfig.PUBLICTHRESH))
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index cafbf38c..41cdf819 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -2127,7 +2127,7 @@ class DisplayMappingResults(object):
                 tableIterationsCnt = tableIterationsCnt + 1
 
                 this_row = [] #container for the cells of each row
-                selectCheck = HT.Input(type="checkbox", name="searchResult", value=theGO["GeneSymbol"], Class="checkbox trait_checkbox") #checkbox for each row
+                selectCheck = HT.Input(type="checkbox", name="selectCheck", value=theGO["GeneSymbol"], Class="checkbox trait_checkbox") #checkbox for each row
 
                 geneLength = (theGO["TxEnd"] - theGO["TxStart"])*1000.0
                 tenPercentLength = geneLength*0.0001
@@ -2213,7 +2213,7 @@ class DisplayMappingResults(object):
         elif self.dataset.group.species == 'rat':
             for gIndex, theGO in enumerate(geneCol):
                 this_row = [] #container for the cells of each row
-                selectCheck = HT.Input(type="checkbox", name="searchResult", Class="checkbox", onClick="highlight(this)").__str__() #checkbox for each row
+                selectCheck = HT.Input(type="checkbox", name="selectCheck", Class="checkbox trait_checkbox").__str__() #checkbox for each row
 
                 #ZS: May want to get this working again later
                 #webqtlSearch = HT.Href(os.path.join(webqtlConfig.CGIDIR, webqtlConfig.SCRIPTFILE)+"?cmd=sch&gene=%s&alias=1&species=rat" % theGO["GeneSymbol"], ">>", target="_blank").__str__()
@@ -2240,14 +2240,14 @@ class DisplayMappingResults(object):
                 #Mouse Gene
                 if theGO['mouseGene']:
                     mouseChr = theGO['mouseGene']["Chromosome"]
-                    mouseTxStart = theGO['mouseGene']["TxStart"]
+                    mouseTxStart = "%0.6f" % theGO['mouseGene']["TxStart"]
                 else:
                     mouseChr = mouseTxStart = ""
 
                 #the chromosomes for human 1 are 1qXX.XX
                 if theGO['humanGene']:
                     humanChr = theGO['humanGene']["Chromosome"]
-                    humanTxStart = theGO['humanGene']["TxStart"]
+                    humanTxStart = "%0.6f" % theGO['humanGene']["TxStart"]
                 else:
                     humanChr = humanTxStart = ""
 
@@ -2258,7 +2258,7 @@ class DisplayMappingResults(object):
                 this_row = [selectCheck.__str__(),
                             str(gIndex+1),
                             geneSymbolNCBI,
-                            theGO["TxStart"],
+                            "%0.6f" % theGO["TxStart"],
                             HT.Href(geneLengthURL, "%0.3f" % (geneLength*1000.0)).__str__(),
                             avgExprVal,
                             mouseChr,
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 0f37e711..4e3c203d 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -73,50 +73,51 @@ 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/%s.txt -a %s/%s_snps.txt -gk > %s/gn2/%s.json' % (flat_files('genotype/bimbam'),
-          #                                                                                genofile_name,
-          #                                                                                flat_files('genotype/bimbam'),
-          #                                                                                trait_filename,
-          #                                                                                flat_files('genotype/bimbam'),
-          #                                                                                genofile_name,
-          #                                                                                TEMPDIR,
-          #                                                                                k_output_filename)
+        #   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,
+                                                                                         trait_filename,
+                                                                                         flat_files('genotype/bimbam'),
+                                                                                         genofile_name,
+                                                                                         TEMPDIR,
+                                                                                         k_output_filename)
 
           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_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 + ' -g %s/%s_geno.txt -p %s/%s_pheno.txt' % (flat_files('genotype/bimbam'),
-          #                                                                                genofile_name,
-          #                                                                                flat_files('genotype/bimbam'),
-          #                                                                                genofile_name)
+          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'),
+                                                                                         genofile_name,
+                                                                                         TEMPDIR,
+                                                                                         trait_filename)
 
 
           if covariates != "":
-              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' % (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)
 
 
       logger.debug("gemma_command:" + gemma_command)
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index e10b31c0..5178ece8 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -168,7 +168,7 @@ class ShowTrait(object):
                 hddn['control_marker'] = self.nearest_marker
                 #hddn['control_marker'] = self.nearest_marker1+","+self.nearest_marker2
         hddn['do_control'] = False
-        hddn['maf'] = 0.01
+        hddn['maf'] = 0.05
         hddn['compare_traits'] = []
         hddn['export_data'] = ""
         hddn['export_format'] = "excel"
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index 21fc99d3..3fd9faf5 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -127,27 +127,35 @@
           <a href="http://joss.theoj.org/papers/10.21105/joss.00025"><img src="https://camo.githubusercontent.com/846b750f582ae8f1d0b4f7e8fee78bed705c88ba/687474703a2f2f6a6f73732e7468656f6a2e6f72672f7061706572732f31302e32313130352f6a6f73732e30303032352f7374617475732e737667" alt="JOSS" data-canonical-src="http://joss.theoj.org/papers/10.21105/joss.00025/status.svg" style="max-width:100%;"></a>
         </p>
           <br />
-        <p>GeneNetwork is supported by:</p>
-        <UL>
-            <LI>
-                <a  href="http://citg.uthsc.edu">
+        <p>GeneNetwork support from:</p>
+        <ul>
+            <li>
+                <a href="http://citg.uthsc.edu">
                     The UT Center for Integrative and Translational Genomics
-                </A>
+                </a>
             </li>
-            <LI><a  href="http://www.iniastress.org">NIAAA</A>
-                Integrative Neuroscience Initiative on Alcoholism
-                (U01 AA016662, U01 AA013499, U24 AA013513, U01 AA014425)
+            <li>
+                <a href="https://www.nigms.nih.gov/">NIGMS</a>
+                Systems Genetics and Precision Medicine Project (R01 GM123489, 2017-2021)
             </li>
-            <LI>
-                <a
-                   href="https://www.drugabuse.gov/">NIDA</A>, <a class="smallsize"  href="http://www.nimh.nih.gov/">NIMH</A>
-                   , and <a class="smallsize"  href="http://www.niaaa.nih.gov/">
-                   NIAAA</A> (P20-DA 21131)
+            <li>
+                <a href="https://www.drugabuse.gov/">NIDA</a>
+                NIDA Core Center of Excellence in Transcriptomics, Systems Genetics, and the Addictome (P30 DA044223, 2017-2022)
             </li>
-            <LI>NCI <a  href="http://emice.nci.nih.gov/">MMHCC</A> (U01CA105417) and
-                <a  href="https://en.wikipedia.org/wiki/National_Center_for_Research_Resources">NCRR</a>
-                <a  href="https://en.wikipedia.org/wiki/Biomedical_Informatics_Research_Network">BIRN</a>
-                (U24 RR021760)
+            <li>
+                <a href="http://www.nia.nih.gov/">NIA</a>
+                Translational Systems Genetics of Mitochondria, Metabolism, and Aging (R01AG043930, 2013-2018)
+            </li>
+            <li>
+                <a href="http://www.iniastress.org/">NIAAA</a>
+                Integrative Neuroscience Initiative on Alcoholism (U01 AA016662, U01 AA013499, U24 AA013513, U01 AA014425, 2006-2017)
+            </li>
+            <li>
+                <a href="http://www.drugabuse.gov/">NIDA</a>, <a href="http://www.nimh.nih.gov/">NIMH</a>, and <a href="http://www.niaaa.nih.gov/">NIAAA</a>
+                (P20-DA 21131, 2001-2012)
+            </li>
+            <li>
+                NCI <a href="http://emice.nci.nih.gov/">MMHCC</a> (U01CA105417), NCRR, <a href="http://www.birncommunity.org/">BIRN</a>, (U24 RR021760)
             </li>
         </UL>
         <!--</p>-->
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index ba4d4d7c..00a7b811 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -262,7 +262,7 @@
         <div style="width: 100%;">
           <h2>Interval Analyst</h2>
           <div id="table_container">
-          <table id="interval_analyst" class="table-hover table-striped cell-border dataTable" style="float: left; width:100%;">
+          <table id="trait_table" class="table-hover table-striped cell-border dataTable" style="float: left; width:100%;">
             <thead>
               <tr>
                 {% for header in gene_table_header %}
@@ -322,6 +322,7 @@
     <script type="text/javascript" charset="utf-8">
         $(document).ready( function () {
             console.time("Creating table");
+            {% if selectedChr == -1 %}
             $('#trait_table').DataTable( {
                 "columns": [
                     { "type": "natural", "width": "5%" },
@@ -346,8 +347,8 @@
                 "scrollCollapse": false,
                 "paging": false
             } );
-
-            $('#interval_analyst').dataTable( {
+            {% elif selectedChr != -1 and plotScale =="physic" and (dataset.group.species == 'mouse' or dataset.group.species == 'rat') %}
+            $('#trait_table').dataTable( {
                 "createdRow": function ( row, data, index ) {
                   $('td', row).eq(1).attr("align", "right");
                   $('td', row).eq(3).attr("align", "right");
@@ -384,6 +385,7 @@
                 "scrollCollapse": false,
                 "paging": false
             } );
+            {% endif %}
 
             $('#vector_map_tab').click(function(){
                 $('div#gn1_map_options').hide();