diff options
| -rw-r--r-- | wqflask/utility/elasticsearch_tools.py | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/gemma_mapping.py | 14 | ||||
| -rw-r--r-- | wqflask/wqflask/show_trait/SampleList.py | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/show_trait/show_trait.py | 42 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/show_trait.js | 52 | ||||
| -rwxr-xr-x | wqflask/wqflask/templates/index_page_orig.html | 44 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_trait.html | 1 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_trait_edit_data.html | 20 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/show_trait_mapping_tools.html | 4 | ||||
| -rw-r--r-- | wqflask/wqflask/user_manager.py | 5 |
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 |