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authorzsloan2019-01-16 16:30:11 -0600
committerzsloan2019-01-16 16:30:11 -0600
commita4844e373b9499f5b91913e88eb1314ed19bc582 (patch)
treed21d97b77d6a1dd9366bc14edfc3dec4b45b0250
parentf1ea496ae71388810f0e6dffe36b005ceabaed6c (diff)
downloadgenenetwork2-a4844e373b9499f5b91913e88eb1314ed19bc582.tar.gz
Pushing SNP browser updates
-rw-r--r--wqflask/wqflask/snp_browser/snp_browser.py97
-rw-r--r--wqflask/wqflask/static/new/css/snp_browser.css32
-rw-r--r--wqflask/wqflask/templates/snp_browser.html206
3 files changed, 264 insertions, 71 deletions
diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py
index 0058070c..820551eb 100644
--- a/wqflask/wqflask/snp_browser/snp_browser.py
+++ b/wqflask/wqflask/snp_browser/snp_browser.py
@@ -15,24 +15,25 @@ from base import webqtlConfig
class SnpBrowser(object):
- MAXSNPRETURN = 5000
-
def __init__(self, start_vars):
self.strain_lists = get_browser_sample_lists()
self.initialize_parameters(start_vars)
+ self.limit_number = 10000
if self.first_run == "false":
- if self.limit_strains == "true":
- self.header_fields = get_header_list(self.variant_type, self.chosen_strains)
- else:
- self.header_fields = get_header_list(self.variant_type, self.strain_lists, self.species_name)
self.filtered_results = self.get_browser_results()
- if len(self.filtered_results) <= 5000:
+ if len(self.filtered_results) <= self.limit_number:
self.table_rows = self.get_table_rows()
else:
+ self.empty_columns = None
self.table_rows = []
+ if self.limit_strains == "true":
+ self.header_fields, self.empty_field_count = get_header_list(variant_type = self.variant_type, strains = self.chosen_strains, empty_columns = self.empty_columns)
+ else:
+ self.header_fields, self.empty_field_count = get_header_list(variant_type = self.variant_type, strains = self.strain_lists, species = self.species_name, empty_columns = self.empty_columns)
+
def initialize_parameters(self, start_vars):
if 'first_run' in start_vars:
self.first_run = "false"
@@ -109,7 +110,7 @@ class SnpBrowser(object):
"WSB/EiJ",
"PWK/PhJ",
"CAST/EiJ"]
- self.chosen_strains_rat = ["BN", "F344"]
+ self.chosen_strains_rat = ["BN", "F344", "WLI", "WMI"]
if 'chosen_strains_mouse' in start_vars:
self.chosen_strains_mouse = start_vars['chosen_strains_mouse'].split(",")
if 'chosen_strains_rat' in start_vars:
@@ -165,9 +166,9 @@ class SnpBrowser(object):
query = "SELECT Id, Chromosome, Position, Position+0.000001 FROM SnpAll WHERE Rs = '%s'" % self.gene_name
else:
if self.species_id != 0:
- query = "SELECT Id, Chromosome, Position, Position+0.000001 ForM SnpAll where SpeciesId = %s AND SnpName = '%s'" % (self.species_id, self.gene_name)
+ query = "SELECT Id, Chromosome, Position, Position+0.000001 FROM SnpAll where SpeciesId = %s AND SnpName = '%s'" % (self.species_id, self.gene_name)
else:
- query = "SELECT Id, Chromosome, Position, Position+0.000001 ForM SnpAll where SnpName = '%s'" % (self.gene_name)
+ query = "SELECT Id, Chromosome, Position, Position+0.000001 FROM SnpAll where SnpName = '%s'" % (self.gene_name)
result_snp = g.db.execute(query).fetchall()
if result_snp:
self.snp_list = [item[0] for item in result_snp]
@@ -266,18 +267,18 @@ class SnpBrowser(object):
if self.variant_type == "SNP":
display_strains = []
snp_id, species_id, snp_name, rs, chr, mb, mb_2016, alleles, snp_source, conservation_score = result[:10]
- effect_list = result[10:26]
+ effect_list = result[10:28]
if self.species_id == 1:
- self.allele_list = result[27:]
+ self.allele_list = result[30:]
elif self.species_id == 2:
- self.allele_list = result[28:]
+ self.allele_list = result[31:]
if self.limit_strains == "true" and len(self.chosen_strains) > 0:
for index in strain_index_list:
if self.species_id == 1:
- display_strains.append(result[27+index])
+ display_strains.append(result[29+index])
elif self.species_id == 2:
- display_strains.append(result[28+index])
+ display_strains.append(result[31+index])
self.allele_list = display_strains
effect_info_dict = get_effect_info(effect_list)
@@ -369,8 +370,20 @@ class SnpBrowser(object):
if len(gene_name_list) > 0:
gene_id_name_dict = get_gene_id_name_dict(self.species_id, gene_name_list)
+ #ZS: list of booleans representing which columns are entirely empty, so they aren't displayed on the page; only including ones that are sometimes empty (since there's always a location, etc)
+ self.empty_columns = {
+ "snp_source": "false",
+ "conservation_score": "false",
+ "gene_name": "false",
+ "transcript": "false",
+ "exon": "false",
+ "domain_2": "false",
+ "function": "false",
+ "function_details": "false"
+ }
+
the_rows = []
- for result in self.filtered_results:
+ for i, result in enumerate(self.filtered_results):
this_row = []
if self.variant_type == "SNP":
snp_name, rs, chr, mb, alleles, gene, transcript, exon, domain, function, function_details, snp_source, conservation_score, snp_id = result[:14]
@@ -395,11 +408,14 @@ class SnpBrowser(object):
source_url_1 = "http://www.sanger.ac.uk/resources/mouse/genomes/"
source_url_2 = "http://mouse.cs.ucla.edu/mousehapmap/beta/wellcome.html"
source_urls = [source_url_1, source_url_2]
+ self.empty_columns['snp_source'] = "true"
else:
source_urls = []
if not conservation_score:
conservation_score = ""
+ else:
+ self.empty_columns['conservation_score'] = "true"
if gene:
gene_name = gene[1]
@@ -409,17 +425,21 @@ class SnpBrowser(object):
gene_link = webqtlConfig.NCBI_LOCUSID % gene_id
else:
gene_link = "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=gene&term=%s" % gene_name
+
+ self.empty_columns['gene_name'] = "true"
else:
gene_name = ""
gene_link = ""
if transcript:
transcript_link = webqtlConfig.ENSEMBLETRANSCRIPT_URL % (transcript)
+ self.empty_columns['transcript'] = "true"
else:
transcript_link = ""
if exon:
exon = exon[1] # exon[0] is exon_id, exon[1] is exon_rank
+ self.empty_columns['exon'] = "true"
else:
exon = ""
@@ -432,6 +452,12 @@ class SnpBrowser(object):
if domain_1 == "Exon":
domain_1 = domain_1 + " " + exon
+ if domain_2 != "":
+ self.empty_columns['domain_2'] = "true"
+
+ if function:
+ self.empty_columns['function'] = "true"
+
function_list = []
if function_details:
function_list = string.split(string.strip(function_details), ",")
@@ -442,6 +468,8 @@ class SnpBrowser(object):
function_details = function_details.replace("/", " -> ")
if function_details == "Biotype: Protein Coding":
function_details = function_details + ", Coding Region Unknown"
+
+ self.empty_columns['function_details'] = "true"
#[snp_href, chr, mb_formatted, alleles, snp_source_cell, conservation_score, gene_name_cell, transcript_href, exon, domain_1, domain_2, function, function_details]
@@ -459,6 +487,7 @@ class SnpBrowser(object):
the_bases.append(this_base)
this_row = {
+ "index": i + 1,
"rs": rs,
"snp_url": snp_url,
"snp_name": snp_name,
@@ -483,6 +512,7 @@ class SnpBrowser(object):
elif self.variant_type == "InDel":
indel_name, indel_chr, indel_mb_s, indel_mb_e, indel_strand, indel_type, indel_size, indel_sequence, source_name = result
this_row = {
+ "index": i,
"indel_name": indel_name,
"indel_chr": indel_chr,
"indel_mb_s": indel_mb_s,
@@ -637,7 +667,7 @@ def get_browser_sample_lists(species_id=1):
return strain_lists
-def get_header_list(variant_type, strains, species = None):
+def get_header_list(variant_type, strains, species = None, empty_columns = None):
if species == "Mouse":
strain_list = strains['mouse']
elif species == "Rat":
@@ -645,14 +675,43 @@ def get_header_list(variant_type, strains, species = None):
else:
strain_list = strains
+ empty_field_count = 0 #ZS: This is an awkward way of letting the javascript know the index where the allele value columns start; there's probably a better way of doing this
+
header_fields = []
if variant_type == "SNP":
header_fields.append(['Index', 'SNP ID', 'Chr', 'Mb', 'Alleles', 'Source', 'ConScore', 'Gene', 'Transcript', 'Exon', 'Domain 1', 'Domain 2', 'Function', 'Details'])
header_fields.append(strain_list)
+
+ if empty_columns != None:
+ if empty_columns['snp_source'] == "false":
+ empty_field_count += 1
+ header_fields[0].remove('Source')
+ if empty_columns['conservation_score'] == "false":
+ empty_field_count += 1
+ header_fields[0].remove('ConScore')
+ if empty_columns['gene_name'] == "false":
+ empty_field_count += 1
+ header_fields[0].remove('Gene')
+ if empty_columns['transcript'] == "false":
+ empty_field_count += 1
+ header_fields[0].remove('Transcript')
+ if empty_columns['exon'] == "false":
+ empty_field_count += 1
+ header_fields[0].remove('Exon')
+ if empty_columns['domain_2'] == "false":
+ empty_field_count += 1
+ header_fields[0].remove('Domain 2')
+ if empty_columns['function'] == "false":
+ empty_field_count += 1
+ header_fields[0].remove('Function')
+ if empty_columns['function_details'] == "false":
+ empty_field_count += 1
+ header_fields[0].remove('Details')
+
elif variant_type == "InDel":
header_fields = ['Index', 'ID', 'Type', 'InDel Chr', 'Mb Start', 'Mb End', 'Strand', 'Size', 'Sequence', 'Source']
- return header_fields
+ return header_fields, empty_field_count
def get_effect_details_by_category(effect_name = None, effect_value = None):
gene_list = []
@@ -709,7 +768,7 @@ def get_effect_info(effect_list):
effect_info_dict = {}
prime3_utr, prime5_utr, upstream, downstream, intron, nonsplice_site, splice_site, intergenic = effect_list[:8]
- exon, non_synonymous_coding, synonymous_coding, start_gained, start_lost, stop_gained, stop_lost, unknown_effect_in_exon = effect_list[8:]
+ exon, non_synonymous_coding, synonymous_coding, start_gained, start_lost, stop_gained, stop_lost, unknown_effect_in_exon = effect_list[8:16]
if intergenic:
domain = "Intergenic"
diff --git a/wqflask/wqflask/static/new/css/snp_browser.css b/wqflask/wqflask/static/new/css/snp_browser.css
index c1adaf20..30fe9a59 100644
--- a/wqflask/wqflask/static/new/css/snp_browser.css
+++ b/wqflask/wqflask/static/new/css/snp_browser.css
@@ -19,4 +19,36 @@ table.dataTable thead th{
border-right: 1px solid white;
color: white;
background-color: royalblue;
+}
+
+table.dataTable tbody td {
+ padding: 4px 20px 2px 10px;
+}
+
+td.A_allele_color {
+ background-color: #C33232
+}
+td.C_allele_color {
+ background-color: #1569C7
+}
+td.T_allele_color {
+ background-color: #CFCF32
+}
+td.G_allele_color {
+ background-color: #32C332
+}
+td.t_allele_color {
+ background-color: #FF6
+}
+td.c_allele_color {
+ background-color: #5CB3FF
+}
+td.a_allele_color {
+ background-color: #F66
+}
+td.g_allele_color {
+ background-color: #CF9
+}
+td.default_allele_color {
+ background-color: #FFFFFF
} \ No newline at end of file
diff --git a/wqflask/wqflask/templates/snp_browser.html b/wqflask/wqflask/templates/snp_browser.html
index cbca9d22..8ae763fa 100644
--- a/wqflask/wqflask/templates/snp_browser.html
+++ b/wqflask/wqflask/templates/snp_browser.html
@@ -182,7 +182,7 @@
<div style="margin-top: 20px;">
{% if filtered_results is defined %}
- {% if filtered_results|length > 5000 %}
+ {% if filtered_results|length > limit_number %}
There are more than 5000 results. Consider limiting your search to a smaller range.
{% else %}
<table class="dataTable cell-border nowrap" id="results_table" style="float: left;">
@@ -204,44 +204,7 @@
</tr>
</thead>
<tbody>
- {% for row in table_rows %}
- {% if variant_type == "SNP" %}
- <tr>
- <td><input type="checkbox" name="trait_check"></td>
- <td align="right">{{ loop.index }}</td>
- <td>{% if row.rs != "" %}<b><a href="{{ row.snp_url }}">{{ row.snp_name }}</a></b>{% else %}<a href="{{ row.snp_url }}">{{ row.snp_name }}</a>{% endif %}</td>
- <td>{{ row.chr }}</td>
- <td>{{ row.mb_formatted }}</td>
- <td>{{ row.alleles }}</td>
- <td>{% if row.snp_source == "Sanger/UCLA" %}<a href="{{ row.source_urls[0] }}">Sanger</a>/<a href="{{ row.source_urls[1] }}">UCLA</a>{% else %}{{ row.snp_source }}{% endif %}</td>
- <td>{{ row.conservation_score }}</td>
- <td>{% if row.gene_name != "" %}<i>{{ row.gene_name }}</i><br><a href="{{ row.gene_link }}">NCBI</a>{% else %}{% endif %}</td>
- <td><a href="{{ row.transcript_link }}">{{ row.transcript }}</a></td>
- <td>{{ row.exon }}</td>
- <td>{{ row.domain_1 }}</td>
- <td>{{ row.domain_2 }}</td>
- <td>{{ row.function }}</td>
- <td>{{ row.function_details }}</td>
- {% for item in row.allele_value_list %}
- <td style="background-color: {{ item[1] }};">{{ item[0] }}</td>
- {% endfor %}
- </tr>
- {% else %}
- <tr>
- <td><input type="checkbox" name="trait_check"></td>
- <td align="right">{{ loop.index }}</td>
- <td>{{ row.indel_name }}</td>
- <td>{{ row.indel_type }}</td>
- <td>{{ row.indel_chr }}</td>
- <td>{{ row.indel_mb_s }}</td>
- <td>{{ row.indel_mb_e }}</td>
- <td>{{ row.indel_strand }}</td>
- <td>{{ row.indel_size }}</td>
- <td>{{ row.indel_sequence }}</td>
- <td>{{ row.source_name }}</td>
- </tr>
- {% endif %}
- {% endfor %}
+ <td colspan="100%" align="center"><br><b><font size="15">Loading...</font></b><br></td>
</tbody>
</table>
{% endif %}
@@ -253,26 +216,165 @@
{% block js %}
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.js"></script>
<script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
+
+ <script type='text/javascript'>
+ var json_rows = {{ table_rows|safe }};
+ var empty_columns = {{ empty_columns|safe }};
+ </script>
+
<script language="javascript">
{% if filtered_results is defined %}
$("#results_table").DataTable( {
+ 'data': json_rows,
{% if variant_type == "SNP" %}
- "columnDefs": [ {
- "targets": [0, {% for n in range(15, 15 + allele_list|length) %}, {{ n }}{% endfor %}],
- "orderable": false
- } ],
+ 'columns': [
+ {
+ 'data': null,
+ 'orderable': false,
+ 'render': function(data, type, row, meta) {
+ return '<input type="checkbox" name="trait_check">'
+ }
+ }, {
+ 'data': 'index'
+ }, {
+ 'data': null,
+ 'render': function(data, type, row, meta) {
+ if (data.rs != "") {
+ return '<b><a href="' + data.snp_url + '">' + data.snp_name + '</a></b>'
+ } else {
+ return '<a href="' + data.snp_url + '">' + data.snp_name + '</a>'
+ }
+ }
+ }, {
+ 'data': 'chr'
+ }, {
+ 'data': 'mb_formatted'
+ }, {
+ 'data': 'alleles'
+ }, {% if empty_columns['snp_source'] == "true" %}{
+ 'data': null,
+ 'render': function(data, type, row, meta) {
+ if (data.snp_source == "Sanger/UCLA") {
+ return '<a href="' + data.source_urls[0] + '">Sanger</a><a href="' + data.source_urls[1] + '">UCLA</a>'
+ } else {
+ return data.snp_source
+ }
+ }
+ }, {% endif %} {% if empty_columns['conservation_score'] == "true" %}{
+ 'data': 'conservation_score'
+ }, {% endif %} {% if empty_columns['gene_name'] == "true" %}{
+ 'data': null,
+ 'render': function(data, type, row, meta) {
+ if (data.gene_name != "") {
+ return '<i>' + data.gene_name + '</i><br><a href="' + data.gene_link + '">NCBI</a>'
+ } else {
+ return data.gene_name
+ }
+ }
+ }, {% endif %} {% if empty_columns['transcript'] == "true" %}{
+ 'data': null,
+ 'render': function(data, type, row, meta) {
+ if (data.transcript != "") {
+ return '<a href="' + data.transcript_link + '">' + data.transcript + '</a>'
+ } else {
+ return data.transcript
+ }
+ }
+ }, {% endif %} {% if empty_columns['exon'] == "true" %}{
+ 'data': 'exon'
+ }, {% endif %}{
+ 'data': 'domain_1'
+ }, {% if empty_columns['domain_2'] == "true" %}{
+ 'data': 'domain_2'
+ }, {% endif %} {% if empty_columns['function'] == "true" %}{
+ 'data': 'function'
+ }, {% endif %} {% if empty_columns['function_details'] == "true" %}{
+ 'data': 'function_details'
+ }, {% endif %} {% for item in allele_list %} {
+ 'data': null,
+ 'orderable': false,
+ 'render': function(data, type, row, meta) {
+ if (typeof data.allele_value_list[{{ loop.index - 1 }}][0] !== "undefined") {
+ return data.allele_value_list[{{ loop.index - 1 }}][0]
+ } else {
+ return ''
+ }
+ }
+ }{% if loop.index < allele_list|length %},{% endif %}{% endfor %}
+ ],
+ 'createdRow': function( row, data, dataIndex) {
+ $('td', row).eq(0).attr("style", "text-align: center; padding: 4px 10px 2px 10px;");
+ $('td', row).eq(1).attr("align", "right");
+ for (i = {{ 15 - empty_field_count }}; i < ({{ 15 - empty_field_count }} + {{ allele_list|length }}); i++) {
+ var this_allele = $('td', row).eq(i).text();
+ $('td', row).eq(i).attr("style", "text-align: center; padding: 4px 10px 2px 10px;");
+ switch (this_allele) {
+ case "A":
+ $('td', row).eq(i).addClass('A_allele_color');
+ break;
+ case "C":
+ $('td', row).eq(i).addClass('C_allele_color');
+ break;
+ case "T":
+ $('td', row).eq(i).addClass('T_allele_color');
+ break;
+ case "G":
+ $('td', row).eq(i).addClass('G_allele_color');
+ break;
+ case "t":
+ $('td', row).eq(i).addClass('t_allele_color');
+ break;
+ case "c":
+ $('td', row).eq(i).addClass('c_allele_color');
+ break;
+ case "a":
+ $('td', row).eq(i).addClass('a_allele_color');
+ break;
+ case "g":
+ $('td', row).eq(i).addClass('g_allele_color');
+ break;
+ default:
+ $('td', row).eq(i).addClass('default_allele_color');
+ }
+ }
+ },
{% else %}
- "columnDefs": [ {
- "targets": 0,
- "orderable": false
- } ],
+ 'columns': [
+ {
+ 'data': null,
+ 'render': function(data, type, row, meta) {
+ return '<input type="checkbox" name="trait_check">'
+ }
+ }, {
+ 'data': 'indel_name'
+ }, {
+ 'data': 'indel_type'
+ }, {
+ 'data': 'indel_chr'
+ }, {
+ 'data': 'indel_mb_s'
+ }, {
+ 'data': 'indel_mb_e'
+ }, {
+ 'data': 'strand'
+ }, {
+ 'data': 'size'
+ }, {
+ 'data': 'sequence'
+ }, {
+ 'data': 'source_name'
+ }
+ ],
{% endif %}
- "order": [[1, "asc" ]],
- "sDom": "tir",
- "iDisplayLength": -1,
- "autoWidth": true,
- "paging": false
+ 'order': [[1, "asc" ]],
+ 'sDom': "rti",
+ 'iDisplayLength': -1,
+ 'processing': true,
+ 'language': {
+ 'loadingRecords': '&nbsp;',
+ 'processing': 'Loading...'
+ }
});
{% endif %}