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-rw-r--r--wqflask/wqflask/snp_browser/snp_browser.py177
-rw-r--r--wqflask/wqflask/static/new/css/main.css45
-rw-r--r--wqflask/wqflask/static/new/javascript/dataset_menu_structure.json111
-rw-r--r--wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js2
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait.js6
-rw-r--r--wqflask/wqflask/templates/base.html35
-rw-r--r--wqflask/wqflask/templates/show_trait_details.html2
-rw-r--r--wqflask/wqflask/templates/show_trait_mapping_tools.html4
-rw-r--r--wqflask/wqflask/templates/snp_browser.html5
9 files changed, 217 insertions, 170 deletions
diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py
index 393b8507..0e999ba2 100644
--- a/wqflask/wqflask/snp_browser/snp_browser.py
+++ b/wqflask/wqflask/snp_browser/snp_browser.py
@@ -1,8 +1,11 @@
from __future__ import absolute_import, print_function, division
-from flask import Flask, g
+from flask import Flask, g, url_for
+
+from htmlgen import HTMLgen2 as HT
import string
+import piddle as pid
from utility.logger import getLogger
logger = getLogger(__name__ )
@@ -31,99 +34,110 @@ class SnpBrowser(object):
self.table_rows = []
def initialize_parameters(self, start_vars):
- self.first_run = "true"
- self.allele_list = []
- if 'variant' in start_vars: #ZS: Check if not first time loaded (if it has form input)
+ if 'first_run' in start_vars:
self.first_run = "false"
+ else:
+ self.first_run = "true"
+ self.allele_list = []
+
+ self.variant_type = "SNP"
+ if 'variant' in start_vars:
self.variant_type = start_vars['variant']
+
+ self.species_name = "Mouse"
+ self.species_id = 1
+ if 'species' in start_vars:
self.species_name = start_vars['species']
- if self.species_name.capitalize() == "Mouse":
- self.species_id = 1
- elif self.species_name.capitalize() == "Rat":
+ if self.species_name.capitalize() == "Rat":
self.species_id = 2
+
+ species_ob = species.TheSpecies(species_name=self.species_name)
+
+ self.chr_list = []
+ for key in species_ob.chromosomes.chromosomes:
+ self.chr_list.append(species_ob.chromosomes.chromosomes[key].name)
+
+ if self.first_run == "true":
+ self.chr = "19"
+ self.start_mb = 30.1
+ self.end_mb = 30.12
+ else:
+ if 'gene_name' in start_vars:
+ if start_vars['gene_name'] != "":
+ self.gene_name = start_vars['gene_name']
+ else:
+ self.gene_name = ""
+ self.chr = start_vars['chr']
+ try:
+ self.start_mb = float(start_vars['start_mb'])
+ self.end_mb = float(start_vars['end_mb'])
+ except:
+ self.start_mb = 0.0
+ self.end_mb = 0.0
else:
- self.species_id = 0 #Using this to indicate "All Species"
-
- #ZS: Currently this is just assuming mouse for determining the chromosomes.
- # This logic may have to change depending upon what other species are added
- self.chr_list = []
- species_ob = species.TheSpecies(species_name="Mouse")
- for key in species_ob.chromosomes.chromosomes:
- self.chr_list.append(species_ob.chromosomes.chromosomes[key].name)
-
- if start_vars['gene_name'] != "":
- self.gene_name = start_vars['gene_name']
- else:
- self.gene_name = ""
- self.chr = start_vars['chr']
try:
+ self.chr = start_vars['chr']
self.start_mb = float(start_vars['start_mb'])
self.end_mb = float(start_vars['end_mb'])
except:
+ self.chr = "1"
self.start_mb = 0.0
self.end_mb = 0.0
- if 'limit_strains' in start_vars:
- self.limit_strains = "true"
- else:
+ self.limit_strains = "true"
+ if self.first_run == "false":
+ if 'limit_strains' not in start_vars:
self.limit_strains = "false"
+ else:
+ if start_vars['limit_strains'] == "false":
+ self.limit_strains = "false"
+
+ self.chosen_strains_mouse = ["C57BL/6J",
+ "DBA/2J",
+ "A/J",
+ "129S1/SvImJ",
+ "NOD/ShiLtJ",
+ "NZO/HlLtJ",
+ "WSB/EiJ",
+ "PWK/PhJ",
+ "CAST/EiJ"]
+ self.chosen_strains_rat = ["BN", "F344"]
+ if 'chosen_strains_mouse' in start_vars:
self.chosen_strains_mouse = start_vars['chosen_strains_mouse'].split(",")
+ if 'chosen_strains_rat' in start_vars:
self.chosen_strains_rat = start_vars['chosen_strains_rat'].split(",")
- if self.species_id == 1:
- self.chosen_strains = self.chosen_strains_mouse
- elif self.species_id == 2:
- self.chosen_strains = self.chosen_strains_rat
+ if self.species_id == 1:
+ self.chosen_strains = self.chosen_strains_mouse
+ else:
+ self.chosen_strains = self.chosen_strains_rat
+ self.domain = "All"
+ if 'domain' in start_vars:
self.domain = start_vars['domain']
+ self.function = "All"
+ if 'function' in start_vars:
self.function = start_vars['function']
+ self.source = "All"
+ if 'source' in start_vars:
self.source = start_vars['source']
+ self.criteria = ">="
+ if 'criteria' in start_vars:
self.criteria = start_vars['criteria']
+ self.score = 0.0
+ if 'score' in start_vars:
self.score = start_vars['score']
- self.redundant = "false"
- self.diff_alleles = "false"
- if 'redundant' in start_vars:
- self.redundant = "true"
- if 'diff_alleles' in start_vars:
- self.diff_alleles = "true"
-
- else: #ZS: Default values
- self.variant_type = "SNP"
- self.species_name = "Mouse"
- species_ob = species.TheSpecies(species_name=self.species_name)
- self.chr_list = []
- for key in species_ob.chromosomes.chromosomes:
- self.chr_list.append(species_ob.chromosomes.chromosomes[key].name)
-
- self.chr = "19"
- self.start_mb = 30.1
- self.end_mb = 30.12
-
- self.limit_strains = "true"
-
- self.chosen_strains_mouse = ["C57BL/6J",
- "DBA/2J",
- "A/J",
- "129S1/SvImJ",
- "NOD/ShiLtJ",
- "NZO/HlLtJ",
- "WSB/EiJ",
- "PWK/PhJ",
- "CAST/EiJ"]
- self.chosen_strains_rat = ["F344"]
- self.chosen_strains_all = self.chosen_strains_mouse + self.chosen_strains_rat
-
- self.chosen_strains = self.chosen_strains_mouse
-
- self.domain = "All"
- self.function = "All"
- self.source = "All"
- self.criteria = ">="
- self.score = 0.0
-
- self.redundant = "false"
- self.diff_alleles = "true"
+ self.redundant = "false"
+ if self.first_run == "false" and 'redundant' in start_vars:
+ self.redundant = "true"
+ self.diff_alleles = "true"
+ if self.first_run == "false":
+ if 'diff_alleles' not in start_vars:
+ self.diff_alleles = "false"
+ else:
+ if start_vars['diff_alleles'] == "false":
+ self.diff_alleles = "false"
def get_browser_results(self):
self.snp_list = None
@@ -567,6 +581,27 @@ class SnpBrowser(object):
return domain_satisfied and function_satisfied and source_satisfied and score_satisfied and different_alleles_satisfied
+ def snp_density_map(self, query, results):
+
+ canvas_width = 900
+ canvas_height = 200
+ snp_canvas = pid.PILCanvas(size=(canvas_width, canvas_height))
+ left_offset, right_offset, top_offset, bottom_offset = (30, 30, 40, 50)
+ plot_width = canvas_width - left_offset - right_offset
+ plot_height = canvas_height - top_offset - bottom_offset
+ y_zero = top_offset + plot_height/2
+
+ x_scale = plot_width/(self.end_mb - self.start_mb)
+
+ #draw clickable image map
+ #gifmap = HT.Map
+ n_click = 80.0
+ click_step = plot_width/n_click
+ click_mb_step = (self.end_mb - self.start_mb)/n_click
+
+ #for i in range(n_click):
+ # href = url_for('snp_browser', first_run="false", chosen_strains_mouse=self.chosen_strains_mouse, chosen_strains_rat=self.chosen_strains_rat, variant=self.variant_type, species=self.species_name, gene_name=self.gene_name, chr=self.chr, start_mb=self.start_mb, end_mb=self.end_mb, limit_strains=self.limit_strains, domain=self.domain, function=self.function, criteria=self.criteria, score=self.score, diff_alleles=self.diff_alleles)
+
def get_browser_sample_lists(species_id=1):
strain_lists = {}
mouse_strain_list = []
diff --git a/wqflask/wqflask/static/new/css/main.css b/wqflask/wqflask/static/new/css/main.css
index 880395a7..097cd997 100644
--- a/wqflask/wqflask/static/new/css/main.css
+++ b/wqflask/wqflask/static/new/css/main.css
@@ -1,11 +1,36 @@
-.security_box {
- padding-left: 30px;
- padding-right: 30px;
-}
-
-ol {
- font-family: Arial;
- font-weight: bold;
- font-size: 16px;
- color: #000082
+@media (max-width: 10px) {
+ .navbar-header {
+ float: none;
+ }
+ .navbar-toggle {
+ display: block;
+ }
+ .navbar-collapse {
+ border-top: 1px solid transparent;
+ box-shadow: inset 0 1px 0 rgba(255,255,255,0.1);
+ }
+ .navbar-collapse.collapse {
+ display: none!important;
+ }
+ .navbar-nav {
+ float: none!important;
+ margin: 7.5px -15px;
+ }
+ .navbar-nav>li {
+ float: none;
+ }
+ .navbar-nav>li>a {
+ padding-top: 10px;
+ padding-bottom: 10px;
+ }
+ .navbar-text {
+ float: none;
+ margin: 15px 0;
+ }
+ .navbar-collapse.collapse.in {
+ display: block!important;
+ }
+ .collapsing {
+ overflow: hidden!important;
+ }
} \ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
index 1c6791c4..9c806a7f 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
+++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
@@ -2591,21 +2591,6 @@
],
"Liver mRNA": [
[
- "858",
- "EPFLMouseLiverHFDRMA0818",
- "EPFL/LISP BXD HFD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA"
- ],
- [
- "852",
- "NIA-AgBXD-Liv_HFD-0818",
- "NIA Aging BXD HFD Liver Affy Clariom S Gene Level (Aug18) RMA **"
- ],
- [
- "857",
- "EPFLMouseLiverCDHFDRMA0818",
- "EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA"
- ],
- [
"859",
"EPFLMouseLiverCDRMA0818",
"EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA"
@@ -2626,6 +2611,21 @@
"UCLA BXD Liver Affy M430 2.0 (Jan16) RMA"
],
[
+ "858",
+ "EPFLMouseLiverHFDRMA0818",
+ "EPFL/LISP BXD HFD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA"
+ ],
+ [
+ "852",
+ "NIA-AgBXD-Liv_HFD-0818",
+ "NIA Aging BXD HFD Liver Affy Clariom S Gene Level (Aug18) RMA **"
+ ],
+ [
+ "857",
+ "EPFLMouseLiverCDHFDRMA0818",
+ "EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA"
+ ],
+ [
"430",
"EPFLMouseLiverRMA0413",
"EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA"
@@ -2641,6 +2641,11 @@
"EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA"
],
[
+ "433",
+ "EPFLMouseLiverBothExRMA0413",
+ "EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level"
+ ],
+ [
"849",
"EPFLMouseLiverCDEx0413",
"EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level"
@@ -2651,11 +2656,6 @@
"EPFL/LISP BXD HFC Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level"
],
[
- "433",
- "EPFLMouseLiverBothExRMA0413",
- "EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level"
- ],
- [
"700",
"UTHSC-VGX_MmBXDHepatocytesRMA1014",
"UT-VGX Hepatocytes Affy Mouse Gene 1.0 ST Gene Level (Oct14) RMA"
@@ -3672,6 +3672,11 @@
"Retina-RGC-Rheaume": {
"Retina Single-cell RNA-Seq": [
[
+ "866",
+ "UConn-RGC-RSeq_log2-0918",
+ "UConn-Rheaume Retina RGC (Sep18) scRNA-Seq Log2"
+ ],
+ [
"865",
"UConn-RGC-RSeq_r-0918",
"UConn-Rheaume Retina RGC (Sep18) scRNA-Seq Raw"
@@ -3680,11 +3685,6 @@
"867",
"UConn-RGC-RSeq_s-0918",
"UConn-Rheaume Retina RGC (Sep18) scRNA-Seq Siamak"
- ],
- [
- "866",
- "UConn-RGC-RSeq_log2-0918",
- "UConn-Rheaume Retina RGC (Sep18) scRNA-Seq Log2"
]
]
},
@@ -3712,16 +3712,18 @@
},
"rat": {
"HSNIH-Palmer": {
+ "Infralimbic Cortex mRNA": [
+ [
+ "861",
+ "HSNIH-Rat-IL-RSeq-0818",
+ "HSNIH-Palmer Infralimbic Cortex RNA-Seq (Aug18) rlog"
+ ]
+ ],
"Lateral Habenula mRNA": [
[
"862",
"HSNIH-Rat-LHB-RSeq-0818",
"HSNIH-Palmer Lateral Habenula RNA-Seq (Aug18) rlog"
- ],
- [
- "870",
- "HSNIH-Rat-LHB-RSeqlog2-0818",
- "HSNIH-Palmer Lateral Habenula RNA-Seq (Aug18) log2"
]
],
"Nucleus Accumbens mRNA": [
@@ -3729,11 +3731,13 @@
"860",
"HSNIH-Rat-Acbc-RSeq-0818",
"HSNIH-Palmer Nucleus Accumbens Core RNA-Seq (Aug18) rlog"
- ],
+ ]
+ ],
+ "Orbitofrontal Cortex mRNA": [
[
- "868",
- "HSNIH-Rat-Acbc-RSeqlog2-0818",
- "HSNIH-Palmer Nucleus Accumbens Core RNA-Seq (Aug18) log2"
+ "864",
+ "HSNIH-Rat-VoLo-RSeq-0818",
+ "HSNIH-Palmer Orbitofrontal Cortex RNA-Seq (Aug18) rlog"
]
],
"Phenotypes": [
@@ -3743,32 +3747,7 @@
"HSNIH-Palmer Phenotypes"
]
],
- "Prefrontal Cortex mRNA": [
- [
- "869",
- "HSNIH-Rat-IL-RSeqlog2-0818",
- "HSNIH-Palmer Infralimbic Cortex RNA-Seq (Aug18) log2"
- ],
- [
- "872",
- "HSNIH-Rat-VoLo-RSeqlog2-0818",
- "HSNIH-Palmer Orbitofrontal Cortex RNA-Seq (Aug18) log2"
- ],
- [
- "861",
- "HSNIH-Rat-IL-RSeq-0818",
- "HSNIH-Palmer Infralimbic Cortex RNA-Seq (Aug18) rlog"
- ],
- [
- "864",
- "HSNIH-Rat-VoLo-RSeq-0818",
- "HSNIH-Palmer Orbitofrontal Cortex RNA-Seq (Aug18) rlog"
- ],
- [
- "871",
- "HSNIH-Rat-PL-RSeqlog2-0818",
- "HSNIH-Palmer Prelimbic Cortex RNA-Seq (Aug18) log2"
- ],
+ "Prelimbic Cortex mRNA": [
[
"863",
"HSNIH-Rat-PL-RSeq-0818",
@@ -5532,6 +5511,10 @@
"Phenotypes"
],
[
+ "Infralimbic Cortex mRNA",
+ "Infralimbic Cortex mRNA"
+ ],
+ [
"Lateral Habenula mRNA",
"Lateral Habenula mRNA"
],
@@ -5540,8 +5523,12 @@
"Nucleus Accumbens mRNA"
],
[
- "Prefrontal Cortex mRNA",
- "Prefrontal Cortex mRNA"
+ "Orbitofrontal Cortex mRNA",
+ "Orbitofrontal Cortex mRNA"
+ ],
+ [
+ "Prelimbic Cortex mRNA",
+ "Prelimbic Cortex mRNA"
]
],
"HSNIH-RGSMC": [
diff --git a/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js b/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js
index d5ce6f84..3f123d6f 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js
+++ b/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js
@@ -94,7 +94,7 @@ $(function() {
})(this));
open_window = function(url, name) {
var options;
- options = "menubar=1,toolbar=1,location=1,resizable=1,status=1,scrollbars=1,directories=1,width=900";
+ options = "menubar=yes,toolbar=yes,titlebar=yes,location=yes,resizable=yes,status=yes,scrollbars=yes,directories=yes,width=900";
return open(url, name, options).focus();
};
group_info = function() {
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index a3edd0e6..c1b0cef9 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -829,8 +829,10 @@
}
}
+ root.chart_range = [range_bottom, range_top]
+
total_sample_count = 0
- for (i = 0, i < sample_lists.length; i++) {
+ for (i = 0, i < sample_lists.length; i++;) {
total_sample_count += get_sample_vals(sample_lists[i]).length
}
@@ -839,7 +841,7 @@
var layout = {
yaxis: {
- range: [range_bottom, range_top],
+ range: root.chart_range,
},
width: bar_chart_width,
height: 600,
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index 81c04db5..3d03f3b9 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -22,17 +22,22 @@
<body style="width: 100% !important;">
<!-- Navbar ================================================== -->
- <div class="navbar navbar-inverse navbar-static-top pull-left" role="navigation" style="width: 100%;">
-
+ <div class="navbar navbar-inverse navbar-static-top pull-left" role="navigation" style="width: 100%; white-space: nowrap;">
+ <!--<div class="navbar navbar-default" style="width: 100%; white-space: nowrap;">-->
<div class="container-fluid" style="width: 100%;">
<!-- Brand and toggle get grouped for better mobile display -->
+ <!---
<div class="navbar-header">
- <a class="navbar-brand" href="/">GeneNetwork</a>
+ <a class="navbar-brand" href="/">GeneNetwork</a>
</div>
+ -->
<!-- Collect the nav links, forms, and other content for toggling -->
<div>
<ul class="nav navbar-nav">
+ <li class="" style="margin-right: 20px;">
+ <a href="/" style="font-weight: bold;">GeneNetwork</a>
+ </li>
<li class="">
<a href="/intro">Intro</a>
</li>
@@ -55,22 +60,14 @@
<a href="/snp_browser">SNP Browser</a>
</li>
<li class="">
- <a href="/help">Help</a>
- </li>
- <li class="">
- <a href="/news">News</a>
- </li>
- <li class="">
- <a href="/references">References</a>
- </li>
- <li class="">
- <a href="/policies">Policies</a>
- </li>
- <li class="">
- <a href="/links">Links</a>
- </li>
- <li class="">
- <a href="/environments">Environments</a>
+ <a href="/help" class="dropdow-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">Help <span class="caret"></a>
+ <ul class="dropdown-menu">
+ <li><a href="/news">News</a></li>
+ <li><a href="/references">References</a></li>
+ <li><a href="/policies">Policies</a></li>
+ <li><a href="/links">Links</a></li>
+ <li><a href="/environments">Environments</a></li>
+ </ul>
</li>
<li class="">
{% if g.user_session.logged_in %}
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 1e6d41c2..c1f8f824 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -46,7 +46,7 @@
<tr>
<td>Database</td>
<td>
- <a href="http://genenetwork.org/dbdoc/{{ dataset.name }}.html">
+ <a href="http://genenetwork.org/webqtl/main.py?FormID=sharinginfo&InfoPageName={{ dataset.name }}">
{{ dataset.fullname }}
</a>
</td>
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index c2c201e1..72b3b00b 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -61,11 +61,11 @@
<label style="text-align: right;" class="col-xs-3 control-label">Use LOCO</label>
<div style="margin-left:20px;" class="col-xs-6 controls">
<label class="radio-inline">
- <input type="radio" name="use_loco" value="True" checked="">
+ <input type="radio" name="use_loco" value="True">
Yes
</label>
<label class="radio-inline">
- <input type="radio" name="use_loco" value="False">
+ <input type="radio" name="use_loco" value="False" checked="">
No
</label>
</div>
diff --git a/wqflask/wqflask/templates/snp_browser.html b/wqflask/wqflask/templates/snp_browser.html
index 578bd2fc..3608d0fe 100644
--- a/wqflask/wqflask/templates/snp_browser.html
+++ b/wqflask/wqflask/templates/snp_browser.html
@@ -11,6 +11,7 @@
<div class="container" style="border-style: double; position: relative; width: 950px; padding-top: 10px; padding-right: 40px;">
<form id="snp_browser_form" method="get" action="/snp_browser">
+ <input type="hidden" name="first_run" value="{{ first_run }}">
<input type="hidden" name="chosen_strains_mouse" value="{{ chosen_strains_mouse|join(",") }}">
<input type="hidden" name="chosen_strains_rat" value="{{ chosen_strains_rat|join(",") }}">
<div class="col-xs-4" style="padding-left: 0px;">
@@ -18,8 +19,8 @@
<label for="snp_or_indel" style="text-align: right;" class="col-xs-4 col-form-label"><b>Type:</b></label>
<div class="col-xs-8">
<select name="variant">
- <option value="SNP" selected>SNP</option>
- <option value="InDel">InDel</option>
+ <option value="SNP" {% if variant_type == "SNP" %}selected{% endif %}>SNP</option>
+ <option value="InDel" {% if variant_type == "InDel" %}selected{% endif %}>InDel</option>
</select>
</div>
</div>
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 11:45:15 +0000