aboutsummaryrefslogtreecommitdiff
path: root/wqflask
diff options
context:
space:
mode:
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/utility/elasticsearch_tools.py2
-rw-r--r--wqflask/wqflask/marker_regression/gemma_mapping.py14
-rw-r--r--wqflask/wqflask/show_trait/SampleList.py2
-rw-r--r--wqflask/wqflask/show_trait/show_trait.py42
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait.js52
-rwxr-xr-xwqflask/wqflask/templates/index_page_orig.html44
-rw-r--r--wqflask/wqflask/templates/show_trait.html1
-rw-r--r--wqflask/wqflask/templates/show_trait_edit_data.html20
-rw-r--r--wqflask/wqflask/templates/show_trait_mapping_tools.html4
-rw-r--r--wqflask/wqflask/user_manager.py5
10 files changed, 147 insertions, 39 deletions
diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py
index 293a9ae6..15cdd0bc 100644
--- a/wqflask/utility/elasticsearch_tools.py
+++ b/wqflask/utility/elasticsearch_tools.py
@@ -63,7 +63,7 @@ def get_elasticsearch_connection(for_user=True):
es = Elasticsearch([{
"host": ELASTICSEARCH_HOST, "port": ELASTICSEARCH_PORT
- }]) if (ELASTICSEARCH_HOST and ELASTICSEARCH_PORT) else None
+ }], timeout=30, retry_on_timeout=True) if (ELASTICSEARCH_HOST and ELASTICSEARCH_PORT) else None
if for_user:
setup_users_index(es)
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index dc13afc3..5ebab611 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -144,13 +144,16 @@ def parse_gemma_output(genofile_name):
with open("{}{}_output.assoc.txt".format(webqtlConfig.GENERATED_IMAGE_DIR, genofile_name)) as output_file:
for line in output_file:
- if line.startswith("chr"):
+ if line.startswith("chr\t"):
continue
else:
marker = {}
marker['name'] = line.split("\t")[1]
if line.split("\t")[0] != "X" and line.split("\t")[0] != "X/Y":
- marker['chr'] = int(line.split("\t")[0])
+ if "chr" in line.split("\t")[0]:
+ marker['chr'] = int(line.split("\t")[0][3:])
+ else:
+ marker['chr'] = int(line.split("\t")[0])
else:
marker['chr'] = line.split("\t")[0]
marker['Mb'] = float(line.split("\t")[2]) / 1000000
@@ -186,13 +189,16 @@ def parse_loco_output(this_dataset, gwa_output_filename):
for this_file in output_filelist:
with open(this_file) as output_file:
for line in output_file:
- if line.startswith("chr"):
+ if line.startswith("chr\t"):
continue
else:
marker = {}
marker['name'] = line.split("\t")[1]
if line.split("\t")[0] != "X" and line.split("\t")[0] != "X/Y":
- marker['chr'] = int(line.split("\t")[0])
+ if "chr" in line.split("\t")[0]:
+ marker['chr'] = int(line.split("\t")[0][3:])
+ else:
+ marker['chr'] = int(line.split("\t")[0])
if marker['chr'] > previous_chr:
previous_chr = marker['chr']
elif marker['chr'] < previous_chr:
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index 78bb3b42..8dbba530 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -37,7 +37,7 @@ class SampleList(object):
self.get_attributes()
- self.sample_qnorm = get_transform_vals(self.dataset, this_trait)
+ #self.sample_qnorm = get_transform_vals(self.dataset, this_trait)
if self.this_trait and self.dataset and self.dataset.type == 'ProbeSet':
self.get_extra_attribute_values()
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index d6d83c02..7b952af4 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -12,6 +12,8 @@ from collections import OrderedDict
import redis
Redis = redis.StrictRedis()
+import scipy.stats as ss
+
from flask import Flask, g
from htmlgen import HTMLgen2 as HT
@@ -137,6 +139,8 @@ class ShowTrait(object):
self.make_sample_lists()
+ self.qnorm_vals = quantile_normalize_vals(self.sample_groups)
+
# Todo: Add back in the ones we actually need from below, as we discover we need them
hddn = OrderedDict()
@@ -281,6 +285,44 @@ class ShowTrait(object):
self.sample_groups = (primary_samples,)
self.dataset.group.allsamples = all_samples_ordered
+def quantile_normalize_vals(sample_groups):
+ def normf(trait_vals):
+ ranked_vals = ss.rankdata(trait_vals)
+ p_list = []
+ for i, val in enumerate(trait_vals):
+ p_list.append(((i+1) - 0.5)/len(trait_vals))
+
+ z = ss.norm.ppf(p_list)
+ normed_vals = []
+ for rank in ranked_vals:
+ normed_vals.append("%0.3f" % z[int(rank)-1])
+
+ return normed_vals
+
+ qnorm_by_group = []
+ for sample_type in sample_groups:
+ trait_vals = []
+ for sample in sample_type.sample_list:
+ try:
+ trait_vals.append(float(sample.value))
+ except:
+ continue
+
+ qnorm_vals = normf(trait_vals)
+
+ qnorm_vals_with_x = []
+ counter = 0
+ for sample in sample_type.sample_list:
+ if sample.display_value == "x":
+ qnorm_vals_with_x.append("x")
+ else:
+ qnorm_vals_with_x.append(qnorm_vals[counter])
+ counter += 1
+
+ qnorm_by_group.append(qnorm_vals_with_x)
+
+ return qnorm_by_group
+
def get_nearest_marker(this_trait, this_db):
this_chr = this_trait.locus_chr
logger.debug("this_chr:", this_chr)
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 17afc814..5e2ecc33 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -549,6 +549,7 @@
};
$('#block_outliers').click(block_outliers);
reset_samples_table = function() {
+ $('input[name="transform"]').val("");
return $('.trait_value_input').each((function(_this) {
return function(_index, element) {
console.log("value is:", $(element).val());
@@ -559,6 +560,52 @@
})(this));
};
$('#reset').click(reset_samples_table);
+
+ log_normalize_data = function() {
+ return $('.trait_value_input').each((function(_this) {
+ return function(_index, element) {
+ current_value = $(element).data("value");
+ if(isNaN(current_value)) {
+ return current_value
+ } else {
+ $(element).val(Math.log2(current_value).toFixed(3));
+ return Math.log2(current_value).toFixed(3)
+ }
+ };
+ })(this));
+ };
+
+ qnorm_data = function() {
+ return $('.trait_value_input').each((function(_this) {
+ return function(_index, element) {
+ current_value = $(element).data("value");
+ if(isNaN(current_value)) {
+ return current_value
+ } else {
+ $(element).val($(element).data("qnorm"));
+ return $(element).data("qnorm");
+ }
+ };
+ })(this));
+ };
+
+ normalize_data = function() {
+ if ($('#norm_method option:selected').val() == 'log2'){
+ if ($('input[name="transform"]').val() != "log2") {
+ log_normalize_data()
+ $('input[name="transform"]').val("log2")
+ }
+ }
+ else if ($('#norm_method option:selected').val() == 'qnorm'){
+ if ($('input[name="transform"]').val() != "qnorm") {
+ qnorm_data()
+ $('input[name="transform"]').val("qnorm")
+ }
+ }
+ }
+
+ $('#normalize').click(normalize_data);
+
switch_qnorm_data = function() {
return $('.trait_value_input').each((function(_this) {
return function(_index, element) {
@@ -734,7 +781,7 @@
box_data = [trace1, trace2, trace3]
} else {
var box_layout = {
- width: 500,
+ width: 300,
height: 500,
margin: {
l: 50,
@@ -834,7 +881,7 @@
var layout = {
yaxis: {
- range: [range_bottom, range_top]
+ range: [range_bottom, range_top],
},
width: 1200,
height: 500,
@@ -884,6 +931,7 @@
$('#block_outliers').click(edit_data_change);
$('#reset').click(edit_data_change);
$('#qnorm').click(edit_data_change);
+ $('#normalize').click(edit_data_change);
return console.log("end");
});
diff --git a/wqflask/wqflask/templates/index_page_orig.html b/wqflask/wqflask/templates/index_page_orig.html
index 2a5556ea..dba3e266 100755
--- a/wqflask/wqflask/templates/index_page_orig.html
+++ b/wqflask/wqflask/templates/index_page_orig.html
@@ -34,11 +34,11 @@
<div class="form-group">
<label for="species" class="col-xs-1 control-label" style="width: 65px !important;">Species:</label>
- <div class="col-xs-10 controls input-append" style="padding-right: 0px;">
- <div class="col-xs-8">
- <select name="species" id="species" class="form-control span3" style="width: 280px !important;"></select>
+ <div class="col-xs-10 controls input-append" style="display: flex; padding-left: 20px;">
+ <div class="col-8">
+ <select name="species" id="species" class="form-control" style="width: 280px !important;"></select>
</div>
- <div class="col-xs-4">
+ <div class="col-4" style="margin-left: 10px;">
<button type="button" id="make_default" class="btn btn-primary form-control">Make Default</button>
</div>
</div>
@@ -46,9 +46,9 @@
<div class="form-group">
<label for="group" class="col-xs-1 control-label" style="width: 65px !important;">Group:</label>
- <div class="col-xs-10 controls input-append">
- <div class="col-xs-8">
- <select name="group" id="group" class="form-control span3" style="width: 280px !important;"></select>
+ <div class="col-xs-10 controls input-append" style="padding-left: 20px;">
+ <div class="col-8">
+ <select name="group" id="group" class="form-control" style="width: 280px !important;"></select>
<i class="icon-question-sign"></i>
</div>
</div>
@@ -56,21 +56,21 @@
<div class="form-group">
<label for="tissue" class="col-xs-1 control-label" style="width: 65px !important;">Type:</label>
- <div class="col-xs-10 controls">
- <div class="col-xs-8">
- <select name="type" id="type" class="form-control span3" style="width: 280px !important;"></select>
+ <div class="col-xs-10 controls" style="padding-left: 20px;">
+ <div class="col-8">
+ <select name="type" id="type" class="form-control" style="width: 280px !important;"></select>
</div>
</div>
</div>
<div class="form-group">
<label for="dataset" class="col-xs-1 control-label" style="width: 65px !important;">Dataset:</label>
- <div class="col-xs-10 controls input-append">
- <div class="col-xs-10">
- <select name="dataset" id="dataset" class="form-control span5" style="width: 340px !important;"></select>
+ <div class="col-xs-10 controls input-append" style="display: flex; padding-left: 20px;">
+ <div class="col-9">
+ <select name="dataset" id="dataset" class="form-control" style="width: 340px !important;"></select>
<i class="icon-question-sign"></i>
</div>
- <div class="col-xs-2">
+ <div class="col-3" style="margin-left: 10px;">
<button type="button" id="dataset_info" class="btn btn-primary form-control" style="width: 75px !important;">Info</button>
</div>
</div>
@@ -85,8 +85,8 @@
<div class="form-group">
<label for="or_search" class="col-xs-1 control-label" style="padding-left: 0px; padding-right: 0px; width: 65px !important;">Get Any:</label>
- <div class="col-xs-10 controls">
- <div class="col-xs-8">
+ <div class="col-xs-10 controls" style="padding-left: 20px;">
+ <div class="col-8">
<textarea onkeydown="pressed(event)" name="search_terms_or" rows="1" class="form-control search-query" style="max-width: 550px; width: 450px !important;" id="or_search"></textarea>
</div>
</div>
@@ -95,8 +95,8 @@
<!-- GET ANY HELP -->
<div class="form-group">
<label for="btsearch" class="col-xs-1 control-label" style="width: 65px !important;"></label>
- <div class="col-xs-10 controls">
- <div class="col-xs-12 controls">
+ <div class="col-xs-10 controls" style="padding-left: 20px;">
+ <div class="col-12 controls">
Enter terms, genes, ID numbers in the <b>Search</b> field.<br>
Use <b>*</b> or <b>?</b> wildcards (Cyp*a?, synap*).<br>
Use <b>quotes</b> for terms such as <i>"tyrosine kinase"</i>.
@@ -106,8 +106,8 @@
<div class="form-group">
<label for="and_search" class="col-xs-1 control-label" style="padding-left: 0px; padding-right: 0px; width: 65px !important;">Combined:</label>
- <div class="col-xs-10 controls">
- <div class="col-xs-8">
+ <div class="col-xs-10 controls" style="padding-left: 20px;">
+ <div class="col-8">
<textarea onkeydown="pressed(event)" name="search_terms_and" rows="1" class="form-control search-query" style="max-width: 550px; width: 450px !important;" id="and_search"></textarea>
</div>
</div>
@@ -115,8 +115,8 @@
<div class="form-group">
<label for="btsearch" class="col-xs-1 control-label" style="width: 65px !important;"></label>
- <div class="col-xs-10 controls">
- <div class="col-xs-2 controls" style="width: 100px !important;">
+ <div class="col-xs-10 controls" style="padding-left: 20px;">
+ <div class="col-2 controls" style="width: 100px !important;">
<input id="btsearch" type="submit" class="btn btn-primary form-control" value="Search">
</div>
</div>
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 4aad4242..f67fff90 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -35,6 +35,7 @@
<input type="hidden" name="temp_uuid" id="temp_uuid" value="{{ temp_uuid }}">
<input type="hidden" name="genofile" value="">
<input type="hidden" name="covariates" value="">
+ <input type="hidden" name="transform" value="">
<div class="container">
<div class="panel-group" id="accordion">
diff --git a/wqflask/wqflask/templates/show_trait_edit_data.html b/wqflask/wqflask/templates/show_trait_edit_data.html
index 1402db47..482d1d88 100644
--- a/wqflask/wqflask/templates/show_trait_edit_data.html
+++ b/wqflask/wqflask/templates/show_trait_edit_data.html
@@ -9,7 +9,7 @@
needed.
</p>
- <div id="blockMenuSpan" class="input-append">
+ <div id="blockMenuSpan" class="input-append" style="margin-bottom: 10px;">
<label for="remove_samples_field">Block samples by index:</label>
<input type="text" id="remove_samples_field">
<select id="block_group" size="1">
@@ -25,11 +25,8 @@
<div id="remove_samples_invalid" class="alert alert-error" style="display:none;">
Please check that your input is formatted correctly, e.g. <strong>3, 5-10, 12</strong>
</div>
-
- <br>
-
{% if sample_groups[0].attributes %}
- <div class="input-append">
+ <div class="input-append" style="margin-top:10px; margin-bottom:10px;">
<label for="exclude_menu">Block samples by group:</label>
<select id="exclude_menu" size=1>
{% for attribute in sample_groups[0].attributes %}
@@ -42,7 +39,6 @@
<input type="button" id="exclude_group" class="btn" value="Block">
</div>
{% endif %}
- <br>
<div>
<input type="button" id="hide_no_value" class="btn btn-default" value="Hide No Value">
<input type="button" id="block_outliers" class="btn btn-default" value="Block Outliers">
@@ -55,9 +51,18 @@
</select>
</span>
<br>
+ <div style="margin-top:10px;">
+ <input type="button" id="normalize" class="btn btn-default" value="Normalize">
+ <select id="norm_method" class="select optional span2">
+ <option value="log2">Log2</option>
+ <option value="qnorm">Quantile</option>
+ </select>
+ </div>
+ <!--
{% if sample_groups[0].sample_qnorm is not none %}
<input type="button" id="qnorm" class="btn btn-default" value="Quantile Normalize">
{% endif %}
+ -->
</div>
</fieldset>
<br>
@@ -79,6 +84,7 @@
<!--<div id="edit_sample_lists">-->
{% for sample_type in sample_groups %}
+ {% set outer_loop = loop %}
<div class="sample_group" style="width:{{ trait_table_width }}%;">
<h3>{{ sample_type.header }}</h3>
<hr>
@@ -115,7 +121,7 @@
{# Todo: Add IDs #}
<td class="column_name-Value" align="right">
- <input type="text" data-value="{{ sample.display_value }}" data-transform="{{ sample_type.sample_qnorm[sample.name] }}" name="{{ 'value:' + sample.name }}"
+ <input type="text" data-value="{{ sample.display_value }}" data-qnorm="{{ qnorm_vals[outer_loop.index - 1][loop.index - 1] }}" name="{{ 'value:' + sample.name }}"
style="text-align:right;"
class="trait_value_input edit_sample_value"
value="{{ sample.display_value }}"
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 9c19028c..a54b595b 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -71,8 +71,10 @@
<div class="mapping_method_fields form-group">
<label style="text-align: right;" class="col-xs-3 control-label">Covariates</label>
<div style="margin-left:20px;" class="col-xs-7">
- {% if g.user_session.logged_in and (g.user_session.num_collections > 0) %}
+ {% if g.user_session.logged_in %}
+ {% if g.user_session.num_collections < 1 %}
No collections available. Please add traits to a collection to use them as covariates.
+ {% endif %}
{% elif g.cookie_session.display_num_collections() == "" %}
No collections available. Please add traits to a collection to use them as covariates.
{% else %}
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index 5d388d66..830c7864 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -67,7 +67,10 @@ class AnonUser(object):
# but wouldn't set cookies for staging and my branch. The new code (using @app.after_request) seems to work.
@app.after_request
def set_cookie(response):
- response.set_cookie(self.cookie_name, self.cookie)
+ if self.cookie:
+ pass
+ else:
+ response.set_cookie(self.cookie_name, self.cookie)
return response
#@after.after_this_request