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authorPjotr Prins2015-05-07 09:59:42 -0500
committerPjotr Prins2015-05-07 09:59:42 -0500
commit295c19128073117ba12fa83a89ddba11ae209a3b (patch)
treed91cc4db4c127f0e347d1e170a62a7ec9dc7275d /wqflask
parent4f4ceddafa1d172515b2ef24658e5cf39730e6c6 (diff)
parentde670c307c8f4fcb4758c89fb2b2454e833ecdc8 (diff)
downloadgenenetwork2-295c19128073117ba12fa83a89ddba11ae209a3b.tar.gz
Merge branch 'master' of https://github.com/zsloan/genenetwork2
Diffstat (limited to 'wqflask')
-rwxr-xr-xwqflask/base/trait.py3
-rwxr-xr-xwqflask/wqflask/interval_mapping/interval_mapping.py22
-rw-r--r--wqflask/wqflask/marker_regression/gemma_mapping.py44
-rwxr-xr-xwqflask/wqflask/marker_regression/marker_regression.py31
-rwxr-xr-xwqflask/wqflask/show_trait/show_trait.py41
-rwxr-xr-xwqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee13
-rwxr-xr-xwqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js7
-rwxr-xr-xwqflask/wqflask/templates/new_security/login_user.html43
-rw-r--r--wqflask/wqflask/templates/pair_scan_results.html22
-rwxr-xr-xwqflask/wqflask/templates/search_result_page.html2
-rwxr-xr-xwqflask/wqflask/templates/show_trait_mapping_tools.html12
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>