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

11 files changed, 157 insertions, 83 deletions

diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 58bed865..f3648b80 100755
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -549,6 +549,9 @@ class GeneralTrait(object):
         if self.alias:
             alias = string.replace(self.alias, ";", " ")
             alias = string.join(string.split(alias), ", ")
+        else:
+            alias = 'Not available'
+
         return alias
 
 
diff --git a/wqflask/wqflask/interval_mapping/interval_mapping.py b/wqflask/wqflask/interval_mapping/interval_mapping.py
index 5eb901f7..5511826a 100755
--- a/wqflask/wqflask/interval_mapping/interval_mapping.py
+++ b/wqflask/wqflask/interval_mapping/interval_mapping.py
@@ -57,13 +57,8 @@ class IntervalMapping(object):
         self.set_options(start_vars)
  
         self.json_data = {}
- 
-        #if self.method == "qtl_reaper":
         self.json_data['lodnames'] = ['lod.hk']
         self.gen_reaper_results(tempdata)
-        #else:
-        #    self.gen_pylmm_results(tempdata)
-        #self.gen_qtl_results(tempdata)
 
         #Get chromosome lengths for drawing the interval map plot
         chromosome_mb_lengths = {}
@@ -93,13 +88,7 @@ class IntervalMapping(object):
     def set_options(self, start_vars):
         """Sets various options (physical/genetic mapping, # permutations, which chromosome"""
         
-        #self.plot_scale = start_vars['scale']
-        #if self.plotScale == 'physic' and not fd.genotype.Mbmap:
-        #    self.plotScale = 'morgan'
-        #self.method = start_vars['mapping_method']
         self.num_permutations = int(start_vars['num_perm'])
-        #self.do_bootstrap = start_vars['do_bootstrap']
-        #self.selected_chr = start_vars['chromosome']
         if start_vars['manhattan_plot'] == "true":
             self.manhattan_plot = True
         else:
@@ -112,9 +101,6 @@ class IntervalMapping(object):
             self.control_locus = start_vars['control_locus']
         else:
             self.control_locus = None
-        #self.weighted_regression = start_vars['weighted']
-        #self.lrs_lod = start_vars['lrs_lod']
-
 
     def gen_qtl_results(self, tempdata):
         """Generates qtl results for plotting interval map"""
@@ -134,7 +120,7 @@ class IntervalMapping(object):
         #if self.weighted_regression:
         #    self.lrs_array = self.genotype.permutation(strains = trimmed_samples,
         #                                                         trait = trimmed_values, 
-        #                                                         variance = _vars,
+        #                                                         variance = variances,
         #                                                         nperm=self.num_permutations)
         #else:
         self.lrs_array = genotype.permutation(strains = trimmed_samples,
@@ -175,12 +161,6 @@ class IntervalMapping(object):
         self.json_data['markernames'] = []
         for qtl in reaper_results:
             reaper_locus = qtl.locus
-            #if reaper_locus.chr == "20":
-            #    print("changing to X")
-            #    self.json_data['chr'].append("X")
-            #else:
-            #    self.json_data['chr'].append(reaper_locus.chr)
-            ##self.json_data['chr'].append(reaper_locus.chr)
             self.json_data['pos'].append(reaper_locus.Mb)
             self.json_data['lod.hk'].append(qtl.lrs)
             self.json_data['markernames'].append(reaper_locus.name)
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
new file mode 100644
index 00000000..b1ab780c
--- /dev/null
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -0,0 +1,44 @@
+import os
+
+from base import webqtlConfig
+
+def run_gemma(this_dataset, samples, vals): 
+    """Generates p-values for each marker using GEMMA"""
+        
+    print("INSIDE GEMMA_MAPPING")
+
+    gen_pheno_txt_file(this_dataset, samples, vals)
+
+    os.chdir("{}gemma".format(webqtlConfig.HTMLPATH))
+
+    gemma_command = './gemma -bfile %s -k output_%s.cXX.txt -lmm 1 -o output/%s_output' % (this_dataset.group.name,
+                                                                                    this_dataset.group.name,
+                                                                                    this_dataset.group.name)
+    print("gemma_command:" + gemma_command)
+        
+    os.system(gemma_command)
+        
+    included_markers, p_values = parse_gemma_output(this_dataset)
+
+    return included_markers, p_values
+
+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:
+        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:
+        for line in output_file:
+            if line.startswith("chr"):
+                continue
+            else:
+                included_markers.append(line.split("\t")[1])
+                p_values.append(float(line.split("\t")[10]))
+
+    print("p_values: ", p_values)
+    return included_markers, p_values
\ No newline at end of file
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 67e1df0d..49521bd6 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -32,6 +32,10 @@ from base import data_set
 from base import species
 from base import webqtlConfig
 from utility import webqtlUtil
+#from wqflask.marker_regression import qtl_reaper_mapping
+#from wqflask.marker_regression import plink_mapping
+from wqflask.marker_regression import gemma_mapping
+#from wqflask.marker_regression import rqtl_mapping
 from wqflask.my_pylmm.data import prep_data
 from wqflask.my_pylmm.pyLMM import lmm
 from wqflask.my_pylmm.pyLMM import input
@@ -82,7 +86,10 @@ class MarkerRegression(object):
  
         self.dataset.group.get_markers()
         if self.mapping_method == "gemma":
-            qtl_results = self.run_gemma()
+            included_markers, p_values = gemma_mapping.run_gemma(self.dataset, self.samples, self.vals)
+            self.dataset.group.get_specified_markers(markers = included_markers)
+            self.dataset.group.markers.add_pvalues(p_values)
+            qtl_results = self.dataset.group.markers.markers
         elif self.mapping_method == "rqtl_plink":
             qtl_results = self.run_rqtl_plink()
         elif self.mapping_method == "rqtl_geno":
@@ -97,9 +104,7 @@ class MarkerRegression(object):
 
             if start_vars['pair_scan'] == "true":
                 self.pair_scan = True
-            print("pair scan:", self.pair_scan)
 
-            print("DOING RQTL GENO")
             qtl_results = self.run_rqtl_geno()
             print("qtl_results:", qtl_results)
         elif self.mapping_method == "plink":
@@ -166,11 +171,11 @@ class MarkerRegression(object):
             chromosomes = chromosome_mb_lengths,
             qtl_results = self.filtered_markers,
         )
+        
 
     def run_gemma(self):
         """Generates p-values for each marker using GEMMA"""
         
-        #filename = webqtlUtil.genRandStr("{}_{}_".format(self.dataset.group.name, self.this_trait.name))
         self.gen_pheno_txt_file()
 
         os.chdir("/home/zas1024/gene/web/gemma")
@@ -391,9 +396,23 @@ class MarkerRegression(object):
         return pheno_as_string
 
     def process_pair_scan_results(self, result):
-        results = []
+        pair_scan_results = []
+
+        result = result[1]
+        output = [tuple([result[j][i] for j in range(result.ncol)]) for i in range(result.nrow)]
+        print("R/qtl scantwo output:", output)
+
+        for i, line in enumerate(result.iter_row()):
+            marker = {}
+            marker['name'] = result.rownames[i]
+            marker['chr1'] = output[i][0]
+            marker['Mb'] = output[i][1]
+            marker['chr2'] = int(output[i][2])
+            pair_scan_results.append(marker)
+
+        print("pair_scan_results:", pair_scan_results)
 
-        return results
+        return pair_scan_results
 
     def process_rqtl_results(self, result):        # TODO: how to make this a one liner and not copy the stuff in a loop
         qtl_results = []
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 929f5abb..836a0be5 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -283,13 +283,13 @@ class ShowTrait(object):
         #    else:
         #        pass
 
-        g.db.execute("SELECT Name FROM InbredSet WHERE Name=%s", self.dataset.group.name)
+        result = g.db.execute("SELECT Name FROM InbredSet WHERE Name=%s", self.dataset.group.name)
         if this_trait:
             addSelectionButton = HT.Href(url="#redirect", onClick="addRmvSelection('%s', document.getElementsByName('%s')[0], 'addToSelection');" % (self.dataset.group.name, 'dataInput'))
             addSelectionButton_img = HT.Image("/images/add_icon.jpg", name="addselect", alt="Add To Collection", title="Add To Collection", style="border:none;")
             #addSelectionButton.append(addSelectionButton_img)
             addSelectionText = "Add"
-        elif self.cursor.fetchall():
+        elif result.fetchall():
             addSelectionButton = HT.Href(url="#redirect", onClick="dataEditingFunc(document.getElementsByName('%s')[0], 'addRecord');" % ('dataInput'))
             addSelectionButton_img = HT.Image("/images/add_icon.jpg", name="", alt="Add To Collection", title="Add To Collection", style="border:none;")
             #addSelectionButton.append(addSelectionButton_img)
@@ -368,7 +368,7 @@ class ShowTrait(object):
                         blatsequence = ''
                         for seqt in seqs:
                             if int(seqt[1][-1]) % 2 == 1:
-                                blatsequence += string.strip(seqt[0])
+                                blatsequence += string.strip(seqt[0])## NEEDED FOR UCSC GENOME BROWSER LINK
 
                 #--------Hongqiang add this part in order to not only blat ProbeSet, but also blat Probe
                 blatsequence = '%3E'+this_trait.name+'%0A'+blatsequence+'%0A'
@@ -469,52 +469,25 @@ class ShowTrait(object):
 
             #XZ: Resource Links:
             if this_trait.symbol:
-                linkStyle = "background:#dddddd;padding:2"
-                tSpan = HT.Span(style="font-family:verdana,serif;font-size:13px")
-
                 #XZ,12/26/2008: Gene symbol may contain single quotation mark.
                 #For example, Affymetrix, mouse430v2, 1440338_at, the symbol is 2'-Pde (geneid 211948)
                 #I debug this by using double quotation marks.
                 if _Species == "rat":
-
-                    #XZ, 7/16/2009: The url for SymAtlas (renamed as BioGPS) has changed. We don't need this any more
-                    #symatlas_species = "Rattus norvegicus"
-
-                    #self.cursor.execute("SELECT kgID, chromosome,txStart,txEnd FROM GeneList_rn33 WHERE geneSymbol = '%s'" % this_trait.symbol)
-                    self.cursor.execute('SELECT kgID, chromosome,txStart,txEnd FROM GeneList_rn33 WHERE geneSymbol = "%s"' % this_trait.symbol)
-                    try:
-                        kgId, chr, txst, txen = self.cursor.fetchall()[0]
+                    result = g.db.execute("SELECT kgID, chromosome,txStart,txEnd FROM GeneList_rn33 WHERE geneSymbol = %s", (this_trait.symbol)).fetchone()
+                    if result != None:
+                        kgId, chr, txst, txen = result[0], result[1], result[2], result[3]
                         if chr and txst and txen and kgId:
                             txst = int(txst*1000000)
                             txen = int(txen*1000000)
-                            #tSpan.append(HT.Span(HT.Href(text= 'UCSC',target="mainFrame",\
-                            #        title= 'Info from UCSC Genome Browser', url = webqtlConfig.UCSC_REFSEQ % ('rn3',kgId,chr,txst,txen),Class="fs14 fwn"), style=linkStyle)
-                            #        , " "*2)
-                    except:
-                        pass
                 if _Species == "mouse":
-
-                    #XZ, 7/16/2009: The url for SymAtlas (renamed as BioGPS) has changed. We don't need this any more
-                    #symatlas_species = "Mus musculus"
-
-                    #self.cursor.execute("SELECT chromosome,txStart,txEnd FROM GeneList WHERE geneSymbol = '%s'" % this_trait.symbol)
-                    #try:
                     print("this_trait.symbol:", this_trait.symbol)
                     result = g.db.execute("SELECT chromosome,txStart,txEnd FROM GeneList WHERE geneSymbol = %s", (this_trait.symbol)).fetchone()
                     if result != None:
                         this_chr, txst, txen = result[0], result[1], result[2]
-                    #this_chr, txst, txen = g.db.execute("SELECT chromosome,txStart,txEnd FROM GeneList WHERE geneSymbol = %s", (this_trait.symbol)).fetchone()
                         if this_chr and txst and txen and this_trait.refseq_transcriptid :
                             txst = int(txst*1000000)
                             txen = int(txen*1000000)
-                        #tSpan.append(HT.Span(HT.Href(text= 'UCSC',target="mainFrame",\
-                        #        title= 'Info from UCSC Genome Browser', url = webqtlConfig.UCSC_REFSEQ % ('mm9',
-                        #                                                                                  this_trait.refseq_transcriptid,
-                        #                                                                                  this_chr,
-                        #                                                                                  txst,
-                        #                                                                                  txen),
-                        #        Class="fs14 fwn"), style=linkStyle)
-                        #        , " "*2)
+                        ## NEEDED FOR UCSC GENOME BROWSER LINK
                         
                 #XZ, 7/16/2009: The url for SymAtlas (renamed as BioGPS) has changed. We don't need this any more
                 #tSpan.append(HT.Span(HT.Href(text= 'SymAtlas',target="mainFrame",\
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
index a87d3537..881ea74d 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
@@ -79,8 +79,8 @@ open_mapping_results = (data) ->
     $.colorbox(
         html: data
         href: "#mapping_results_holder"
-        height: "80%"
-        width: "80%"
+        height: "90%"
+        width: "90%"
     )
 
 showalert = (message,alerttype) ->
@@ -154,8 +154,8 @@ $("#plink_compute").click(() =>
         $("#static_progress_bar_container").modal()
         url = "/marker_regression"
         $('input[name=method]').val("plink")
-        $('input[name=mapping_display_all]').val($('input[name=display_all_plink]').val())
-        $('input[name=suggestive]').val($('input[name=suggestive_plink]').val())
+        #$('input[name=mapping_display_all]').val($('input[name=display_all_plink]').val())
+        #$('input[name=suggestive]').val($('input[name=suggestive_plink]').val())
         $('input[name=maf]').val($('input[name=maf_plink]').val())
         form_data = $('#trait_data_form').serialize()
         console.log("form_data is:", form_data)
@@ -164,11 +164,12 @@ $("#plink_compute").click(() =>
 )
 
 $("#gemma_compute").click(() =>
+        console.log("RUNNING GEMMA")
         $("#static_progress_bar_container").modal()
         url = "/marker_regression"
         $('input[name=method]').val("gemma")
-        $('input[name=mapping_display_all]').val($('input[name=display_all_gemma]').val())
-        $('input[name=suggestive]').val($('input[name=suggestive_gemma]').val())
+        #$('input[name=mapping_display_all]').val($('input[name=display_all_gemma]').val())
+        #$('input[name=suggestive]').val($('input[name=suggestive_gemma]').val())
         $('input[name=maf]').val($('input[name=maf_gemma]').val())
         form_data = $('#trait_data_form').serialize()
         console.log("form_data is:", form_data)
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
index c8988cdc..1779df4b 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -99,8 +99,8 @@ open_mapping_results = function(data) {
   return $.colorbox({
     html: data,
     href: "#mapping_results_holder",
-    height: "80%",
-    width: "80%"
+    height: "90%",
+    width: "90%"
   });
 };
 
@@ -187,11 +187,10 @@ $("#plink_compute").click((function(_this) {
 $("#gemma_compute").click((function(_this) {
   return function() {
     var form_data, url;
+    console.log("RUNNING GEMMA");
     $("#static_progress_bar_container").modal();
     url = "/marker_regression";
     $('input[name=method]').val("gemma");
-    $('input[name=mapping_display_all]').val($('input[name=display_all_gemma]').val());
-    $('input[name=suggestive]').val($('input[name=suggestive_gemma]').val());
     $('input[name=maf]').val($('input[name=maf_gemma]').val());
     form_data = $('#trait_data_form').serialize();
     console.log("form_data is:", form_data);
diff --git a/wqflask/wqflask/templates/new_security/login_user.html b/wqflask/wqflask/templates/new_security/login_user.html
index 81e8b53a..a66a85d6 100755
--- a/wqflask/wqflask/templates/new_security/login_user.html
+++ b/wqflask/wqflask/templates/new_security/login_user.html
@@ -24,18 +24,18 @@
             <h4>Already have an account? Sign in here.</h4>
 
 
-            <form class="form-horizontal" action="/n/login" method="POST" name="login_user_form">
+            <form class="form-horizontal" action="/n/login" method="POST" name="login_user_form" id="loginUserForm">
                  <fieldset>
                     <div class="form-group">
                         <label style="text-align:left;" class="col-xs-1 control-label" for="email_address">Email&nbsp;Address</label>
-                        <div style="margin-left:20px;" class="col-xs-10">
+                        <div style="margin-left:20px;" class="col-xs-4">
                             <input id="email_address" class="focused" name="email_address" type="text" value="">
                         </div>
                     </div>
 
                     <div class="form-group">
                         <label style="text-align:left;" class="col-xs-1 control-label" for="password">Password</label>
-                        <div style="margin-left:20px;" class="col-xs-3 controls">
+                        <div style="margin-left:20px;" class="col-xs-4 controls">
                             <input id="password" name="password" type="password" value="">
                             <br />
                             <a href="/n/forgot_password">Forgot your password?</a><br/>
@@ -45,14 +45,14 @@
 
                     <div class="form-group">
                         <label class="col-xs-1 control-label" for="remember"></label>
-                        <div style="margin-left:20px;" class="col-xs-3 controls">
+                        <div style="margin-left:20px;" class="col-xs-4 controls">
                             <input id="remember" name="remember" type="checkbox" value="y"> <b>Remember me</b>
                         </div>
                     </div>
 
                     <div class="form-group">
                         <label class="col-xs-1 control-label" for="submit"></label>
-                        <div style="margin-left:20px;" class="col-xs-3 controls">
+                        <div style="margin-left:20px;" class="col-xs-4 controls">
                             <input id="next" name="next" type="hidden" value="">
                             <input class="btn btn-primary" id="submit" name="submit" type="submit" value="Sign in">
                         </div>
@@ -66,9 +66,42 @@
 
   {% endblock %}
 
+{% block css %}
+<style type="text/css">
+input.error{
+    border:1px solid #FF0000 !important;
+}
+
+label.error,div.error{
+    font-weight:normal;
+    color:#FF0000 !important;
+}
+</style>
+{% endblock %}
+
 {% block js %}
     <!--<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>-->
 
+    <script type="text/javascript" src="/static/new/packages/ValidationPlugin/dist/jquery.validate.min.js"></script>
+    <script>
+    $(document).ready(function () {
+        $("#loginUserForm").validate({
+            onkeyup: false,
+            onsubmit: true,
+            onfocusout: function(element) { $(element).valid(); },
+            rules: {
+                email_address: {
+                    required: true,
+                    email: true
+                },
+                password: {
+                    required: true
+                }
+            }
+        });
+    });
+    </script>
+
     {% include "new_security/_scripts.html" %}
 
 {% endblock %}
diff --git a/wqflask/wqflask/templates/pair_scan_results.html b/wqflask/wqflask/templates/pair_scan_results.html
index 869dabed..f46d7cbf 100644
--- a/wqflask/wqflask/templates/pair_scan_results.html
+++ b/wqflask/wqflask/templates/pair_scan_results.html
@@ -33,6 +33,28 @@
             <h2>
                 Results
             </h2>
+            <table cellpadding="0" cellspacing="0" border="0" id="pair_scan_results" class="table table-hover table-striped table-bordered">
+                <thead>
+                    <tr>
+                        <td>Index</td>
+                        <td>Locus</td>
+                        <td>Chr 1</td>
+                        <td>Mb</td>
+                        <td>Chr 2</td>
+                   </tr>
+                </thead>
+                <tbody>
+                    {% for marker in pair_scan_results %}
+                        <tr>
+                            <td>{{loop.index}}</td>
+                            <td>{{marker.name}}</td>
+                            <td>{{marker.chr1}}</td>
+                            <td>{{marker.Mb}}</td>
+                            <td>{{marker.chr2}}</td>
+                        </tr>
+                    {% endfor %}
+                </tbody>
+            </table>
         </div>
     </div>
 
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 731f6fbd..c7c2a62f 100755
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -42,7 +42,7 @@
             <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"><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>
+            <button class="btn btn-primary"><span class="glyphicon glyphicon-download"></span> Download Table</button>
             <br />
             <br />
             <table class="table table-hover table-striped" id='trait_table'>
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 426a5c5d..27504e51 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -217,16 +217,16 @@
                     <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-1 controls">
+                            <div style="margin-left: 20px;" class="col-xs-2 controls">
                                 <input name="maf_plink" value="0.01" type="text" class="form-control">
                             </div>
                         </div>
                     </div>
                     
                     <div class="form-group">
-                        <label for="gemma_compute" class="col-xs-1 control-label"></label>
+                        <label for="plink_compute" class="col-xs-1 control-label"></label>
                         <div style="margin-left:20px;" class="col-xs-4 controls">
-                            <button id="gemma_compute" class="btn submit_special btn-primary" data-url="/marker_regression" title="Compute Marker Regression">
+                            <button id="plink_compute" class="btn submit_special btn-primary" data-url="/marker_regression" title="Compute Marker Regression">
                                 Compute
                             </button>
                         </div>
@@ -237,16 +237,16 @@
                     <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-1 controls">
+                            <div style="margin-left: 20px;" class="col-xs-2 controls">
                                 <input name="maf_gemma" value="0.01" type="text" class="form-control">
                             </div>
                         </div>
                     </div>
                     
                     <div class="form-group">
-                        <label for="plink_compute" class="col-xs-1 control-label"></label>
+                        <label for="gemma_compute" class="col-xs-1 control-label"></label>
                         <div style="margin-left:20px;" class="col-xs-4 controls">
-                            <button id="plink_compute" class="btn submit_special btn-primary" data-url="/marker_regression" title="Compute Marker Regression">
+                            <button id="gemma_compute" class="btn submit_special btn-primary" data-url="/marker_regression" title="Compute Marker Regression">
                                 Compute
                             </button>
                         </div>