{% endfor %}
{% for strain in header_fields[1] %}
-
{{ strain }}
+
{% for letter in strain|reverse %}
{{ letter }}
{% endfor %}
{% endfor %}
{% else %}
{% for header in header_fields %}
--
cgit v1.2.3
From 7a4068d6d46d923c30316887e1d20f2fa6caa859 Mon Sep 17 00:00:00 2001
From: uditgulati
Date: Fri, 10 Jul 2020 10:15:22 -0500
Subject: add export to CSV button to export current page
---
wqflask/wqflask/templates/snp_browser.html | 43 +++++++++++++++++++++++++++---
1 file changed, 40 insertions(+), 3 deletions(-)
(limited to 'wqflask')
diff --git a/wqflask/wqflask/templates/snp_browser.html b/wqflask/wqflask/templates/snp_browser.html
index 36f893bc..284b55c5 100644
--- a/wqflask/wqflask/templates/snp_browser.html
+++ b/wqflask/wqflask/templates/snp_browser.html
@@ -107,6 +107,12 @@
+
+
+
+
+
+
@@ -192,14 +198,14 @@
{% if header_fields|length == 2 %}
{% for header in header_fields[0] %}
-
{{ header }}
+
{{ header }}
{% endfor %}
{% for strain in header_fields[1] %}
-
{% for letter in strain|reverse %}
{{ letter }}
{% endfor %}
+
{% for letter in strain|reverse %}
{{ letter }}
{% endfor %}
{% endfor %}
{% else %}
{% for header in header_fields %}
-
{{ header }}
+
{{ header }}
{% endfor %}
{% endif %}
@@ -518,6 +524,37 @@
});
$("input[name=chosen_strains]").val(strain_list.join(","));
});
+
+ $("input[name=export_csv]").click(function() {
+ var csv = [];
+ var rows = document.querySelectorAll("table tr");
+
+ var headers = [];
+ var col_header = rows[0].querySelectorAll("th");
+ console.log(col_header.length);
+ for(var i = 1; i < col_header.length; i++) {
+ console.log(col_header[i].getAttribute("name"));
+ headers.push(col_header[i].getAttribute("name"));
+ }
+ csv.push(headers.join(","));
+
+ for (var i = 1; i < rows.length; i++) {
+ var row = [], cols = rows[i].querySelectorAll("td");
+
+ for (var j = 1; j < cols.length; j++)
+ row.push(cols[j].innerText);
+
+ csv.push(row.join(","));
+ }
+
+ var csvFile = new Blob([csv.join("\n")], {type: "text/csv"});
+ var downloadLink = document.createElement("a");
+ downloadLink.download = "hello.csv";
+ downloadLink.href = window.URL.createObjectURL(csvFile);
+ downloadLink.style.display = "none";
+ document.body.appendChild(downloadLink);
+ downloadLink.click();
+ });
{% endblock %}
--
cgit v1.2.3
From f99b69155d35900a75c000fbb79f6bcfb3fa6ff1 Mon Sep 17 00:00:00 2001
From: uditgulati
Date: Fri, 10 Jul 2020 10:30:04 -0500
Subject: export only checked rows to csv; update csv file name
---
wqflask/wqflask/templates/snp_browser.html | 14 ++++++++------
1 file changed, 8 insertions(+), 6 deletions(-)
(limited to 'wqflask')
diff --git a/wqflask/wqflask/templates/snp_browser.html b/wqflask/wqflask/templates/snp_browser.html
index 284b55c5..83606804 100644
--- a/wqflask/wqflask/templates/snp_browser.html
+++ b/wqflask/wqflask/templates/snp_browser.html
@@ -531,25 +531,27 @@
var headers = [];
var col_header = rows[0].querySelectorAll("th");
- console.log(col_header.length);
for(var i = 1; i < col_header.length; i++) {
- console.log(col_header[i].getAttribute("name"));
headers.push(col_header[i].getAttribute("name"));
}
csv.push(headers.join(","));
for (var i = 1; i < rows.length; i++) {
var row = [], cols = rows[i].querySelectorAll("td");
+ var checkBox = rows[i].querySelector("input");
+ console.log(checkBox);
- for (var j = 1; j < cols.length; j++)
- row.push(cols[j].innerText);
+ if(checkBox.checked == true) {
+ for (var j = 1; j < cols.length; j++)
+ row.push(cols[j].innerText);
- csv.push(row.join(","));
+ csv.push(row.join(","));
+ }
}
var csvFile = new Blob([csv.join("\n")], {type: "text/csv"});
var downloadLink = document.createElement("a");
- downloadLink.download = "hello.csv";
+ downloadLink.download = "variant_data.csv";
downloadLink.href = window.URL.createObjectURL(csvFile);
downloadLink.style.display = "none";
document.body.appendChild(downloadLink);
--
cgit v1.2.3
From 349b395375703e727465a1f05f4a5e2d4fc64d2a Mon Sep 17 00:00:00 2001
From: uditgulati
Date: Sun, 19 Jul 2020 17:21:15 -0500
Subject: add server side processing due to large tables in DataTables; work on
server-side processing API pending for sorting, paging etc
---
wqflask/wqflask/snp_browser/snp_browser.py | 39 ++++++++++++++++++++++--------
wqflask/wqflask/templates/snp_browser.html | 26 +++++++++++++++-----
wqflask/wqflask/views.py | 10 ++++++++
3 files changed, 59 insertions(+), 16 deletions(-)
(limited to 'wqflask')
diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py
index a2fb7195..9ae8892b 100644
--- a/wqflask/wqflask/snp_browser/snp_browser.py
+++ b/wqflask/wqflask/snp_browser/snp_browser.py
@@ -4,7 +4,7 @@ import string
from PIL import (Image)
from utility.logger import getLogger
-logger = getLogger(__name__ )
+logger = getLogger(__name__)
from base import species
from base import webqtlConfig
@@ -14,16 +14,16 @@ class SnpBrowser(object):
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":
self.filtered_results = self.get_browser_results()
+ self.table_rows = self.get_table_rows()
+ self.rows_count = len(self.table_rows)
- if len(self.filtered_results) <= self.limit_number:
- self.table_rows = self.get_table_rows()
- else:
- self.empty_columns = None
- self.table_rows = []
+ del self.filtered_results
+
+ if 'sEcho' not in start_vars:
+ self.table_rows = self.table_rows[:500]
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)
@@ -380,7 +380,7 @@ class SnpBrowser(object):
the_rows = []
for i, result in enumerate(self.filtered_results):
- this_row = []
+ 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]
allele_value_list = result[14:]
@@ -520,8 +520,6 @@ class SnpBrowser(object):
"source_name": str(source_name)
}
#this_row = [indel_name, indel_chr, indel_mb_s, indel_mb_e, indel_strand, indel_type, indel_size, indel_sequence, source_name]
- else:
- this_row = {}
the_rows.append(this_row)
@@ -643,6 +641,27 @@ class SnpBrowser(object):
#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)
+class SnpPage(object):
+
+ def __init__(self, start_vars):
+ self.snp_browser = SnpBrowser(start_vars)
+ # self.table_rows = self.filter_rows()
+ self.rows_count = self.snp_browser.rows_count
+ self.sEcho = start_vars['sEcho']
+
+ def filter_rows(self):
+ pass
+
+ def get_page(self):
+ output = {}
+ output['sEcho'] = str(self.sEcho)
+ output['iTotalRecords'] = str(self.rows_count)
+ output['iTotalDisplayRecords'] = str(100)
+ # logger.info(len(self.table_rows), type(self.table_rows), self.table_rows[0])
+ logger.info(self.snp_browser.rows_count, len(self.snp_browser.table_rows))
+ output['data'] = self.snp_browser.table_rows[:100]
+ return output
+
def get_browser_sample_lists(species_id=1):
strain_lists = {}
mouse_strain_list = []
diff --git a/wqflask/wqflask/templates/snp_browser.html b/wqflask/wqflask/templates/snp_browser.html
index 83606804..f3e928af 100644
--- a/wqflask/wqflask/templates/snp_browser.html
+++ b/wqflask/wqflask/templates/snp_browser.html
@@ -188,10 +188,7 @@
- {% if filtered_results is defined %}
- {% if filtered_results|length > limit_number %}
- There are more than 10000 results. Consider limiting your search to a smaller range.
- {% else %}
+ {% if table_rows is defined %}
@@ -214,7 +211,6 @@
Loading...
- {% endif %}
{% endif %}
@@ -229,11 +225,23 @@
-
+
--
cgit v1.2.3
From 4760b390f7e87ea16152a7ecf5422abfb4125176 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 15 Dec 2020 14:36:12 -0600
Subject: Fixed typo in mapping results table
---
wqflask/wqflask/templates/mapping_results.html | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
(limited to 'wqflask')
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 86aa74b0..1a76ef7a 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -389,7 +389,7 @@
"orderable": false
} ],
"language": {
- "info": "Showing1 from _START_ to _END_ of " + js_data.total_markers + " records",
+ "info": "Showing from _START_ to _END_ of " + js_data.total_markers + " records",
},
"order": [[1, "asc" ]],
"sDom": "iRZtir",
--
cgit v1.2.3
From 13ae2b093720a04b63f50a77b92e3b8e480b5ae1 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 15 Dec 2020 14:38:42 -0600
Subject: Added additive effect to GEMMA results + removed an unused function
---
wqflask/wqflask/marker_regression/gemma_mapping.py | 46 ++++------------------
1 file changed, 8 insertions(+), 38 deletions(-)
(limited to 'wqflask')
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 61e4897c..630a3afa 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -80,7 +80,7 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf
os.system(generate_k_command)
- gemma_command = GEMMA_WRAPPER_COMMAND + ' --json --input %s/gn2/%s.json -- ' % (TEMPDIR, k_output_filename) + GEMMAOPTS + ' -a %s/%s_snps.txt -lmm 2 -g %s/%s_geno.txt -p %s/gn2/%s.txt' % (flat_files('genotype/bimbam'),
+ gemma_command = GEMMA_WRAPPER_COMMAND + ' --json --input %s/gn2/%s.json -- ' % (TEMPDIR, k_output_filename) + GEMMAOPTS + ' -a %s/%s_snps.txt -lmm 9 -g %s/%s_geno.txt -p %s/gn2/%s.txt' % (flat_files('genotype/bimbam'),
genofile_name,
flat_files('genotype/bimbam'),
genofile_name,
@@ -101,7 +101,7 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf
marker_obs = parse_loco_output(this_dataset, gwa_output_filename)
return marker_obs, gwa_output_filename
else:
- marker_obs = parse_loco_output(this_dataset, gwa_output_filename)
+ marker_obs = parse_loco_output(this_dataset, gwa_output_filename, use_loco)
return marker_obs, gwa_output_filename
def gen_pheno_txt_file(this_dataset, genofile_name, vals, trait_filename):
@@ -145,41 +145,7 @@ def gen_covariates_file(this_dataset, covariates, samples):
outfile.write(str(this_covariate[i]) + "\t")
outfile.write("\n")
-def parse_gemma_output(genofile_name):
- included_markers = []
- p_values = []
- marker_obs = []
-
- with open("{}{}_output.assoc.txt".format(webqtlConfig.GENERATED_IMAGE_DIR, genofile_name)) as output_file:
- for line in output_file:
- 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":
- 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
- marker['p_value'] = float(line.split("\t")[9])
- if math.isnan(marker['p_value']) or (marker['p_value'] <= 0):
- marker['lod_score'] = 0
- #marker['lrs_value'] = 0
- else:
- marker['lod_score'] = -math.log10(marker['p_value'])
- #marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61
- marker_obs.append(marker)
-
- included_markers.append(line.split("\t")[1])
- p_values.append(float(line.split("\t")[9]))
-
- return marker_obs
-
-def parse_loco_output(this_dataset, gwa_output_filename):
+def parse_loco_output(this_dataset, gwa_output_filename, loco="True"):
output_filelist = []
with open("{}/gn2/".format(TEMPDIR) + gwa_output_filename + ".json") as data_file:
@@ -218,7 +184,11 @@ def parse_loco_output(this_dataset, gwa_output_filename):
else:
marker['chr'] = line.split("\t")[0]
marker['Mb'] = float(line.split("\t")[2]) / 1000000
- marker['p_value'] = float(line.split("\t")[9])
+ if loco == "True":
+ marker['p_value'] = float(line.split("\t")[9])
+ else:
+ marker['p_value'] = float(line.split("\t")[10])
+ marker['additive'] = float(line.split("\t")[7])
if math.isnan(marker['p_value']) or (marker['p_value'] <= 0):
marker['lod_score'] = 0
#marker['lrs_value'] = 0
--
cgit v1.2.3
From 87fdfc19009acda8b58729d0ffbdccbdf6a85a1e Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 16 Dec 2020 11:27:39 -0600
Subject: Set all attribute names to lower-case for sorting in order to keep
order consistent
---
wqflask/wqflask/show_trait/SampleList.py | 4 ++--
wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js | 2 +-
wqflask/wqflask/static/new/javascript/show_trait.js | 2 +-
3 files changed, 4 insertions(+), 4 deletions(-)
(limited to 'wqflask')
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index 00495377..ece485ae 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -108,7 +108,7 @@ class SampleList(object):
FROM CaseAttribute, CaseAttributeXRefNew
WHERE CaseAttributeXRefNew.CaseAttributeId = CaseAttribute.Id
AND CaseAttributeXRefNew.InbredSetId = %s
- ORDER BY CaseAttribute.Name''', (str(self.dataset.group.id),))
+ ORDER BY lower(CaseAttribute.Name)''', (str(self.dataset.group.id),))
self.attributes = {}
for attr, values in itertools.groupby(results.fetchall(), lambda row: (row.Id, row.Name)):
@@ -157,7 +157,7 @@ class SampleList(object):
except ValueError:
pass
- attribute_values[self.attributes[item.Id].name] = attribute_value
+ attribute_values[self.attributes[item.Id].name.lower()] = attribute_value
self.sample_attribute_values[sample_name] = attribute_values
def get_first_attr_col(self):
diff --git a/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js b/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
index 5a4f151c..4362a75e 100644
--- a/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
+++ b/wqflask/wqflask/static/new/javascript/initialize_show_trait_tables.js
@@ -93,7 +93,7 @@ build_columns = function() {
);
}
- attr_keys = Object.keys(js_data.attributes).sort((a, b) => (js_data.attributes[a].name > js_data.attributes[b].name) ? 1 : -1)
+ attr_keys = Object.keys(js_data.attributes).sort((a, b) => (js_data.attributes[a].name.toLowerCase() > js_data.attributes[b].name.toLowerCase()) ? 1 : -1)
for (i = 0; i < attr_keys.length; i++){
column_list.push(
{
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 5dc9e456..98f90f7d 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -571,7 +571,7 @@ populate_sample_attributes_values_dropdown = function() {
sample_attributes = [];
var attributes_as_list = Object.keys(js_data.attributes).map(function(key) {
- return [key, js_data.attributes[key].name];
+ return [key, js_data.attributes[key].name.toLowerCase()];
});
attributes_as_list.sort(function(first, second) {
--
cgit v1.2.3
From 124bc16cdc67b6ba31a281e619dcf15f181ba131 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 16 Dec 2020 11:33:10 -0600
Subject: Removed ID/Sample/Value from Show/Hide Columns in trait page and only
show the option if columns other than those exist
---
wqflask/wqflask/templates/show_trait_edit_data.html | 5 +----
1 file changed, 1 insertion(+), 4 deletions(-)
(limited to 'wqflask')
diff --git a/wqflask/wqflask/templates/show_trait_edit_data.html b/wqflask/wqflask/templates/show_trait_edit_data.html
index 4ad11a5e..0d34bebc 100644
--- a/wqflask/wqflask/templates/show_trait_edit_data.html
+++ b/wqflask/wqflask/templates/show_trait_edit_data.html
@@ -1,12 +1,9 @@
{% for sample_type in sample_groups %}
- {% if loop.index == 1 %}
+ {% if loop.index == 1 and (sample_groups[0].se_exists or has_num_cases or sample_groups[0].attributes|length > 0) %}
Show/Hide Columns:
-
-
-
{% if sample_groups[0].se_exists %}
{% if has_num_cases %}
--
cgit v1.2.3
From ec1e37331e320ed674f184b738b9917753b6071f Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 16 Dec 2020 15:45:53 -0600
Subject: Made change to the way sample table width is calculated to account
for sample name width
---
wqflask/wqflask/show_trait/show_trait.py | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
(limited to 'wqflask')
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 0c6ae198..4c6dd005 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -186,8 +186,6 @@ class ShowTrait(object):
self.has_num_cases = has_num_cases(self.this_trait)
- self.stats_table_width, self.trait_table_width = get_table_widths(self.sample_groups, self.has_num_cases)
-
#ZS: Needed to know whether to display bar chart + get max sample name length in order to set table column width
self.num_values = 0
self.binary = "true" #ZS: So it knows whether to display the Binary R/qtl mapping method, which doesn't work unless all values are 0 or 1
@@ -206,6 +204,8 @@ class ShowTrait(object):
sample_column_width = max_samplename_width * 8
+ self.stats_table_width, self.trait_table_width = get_table_widths(self.sample_groups, sample_column_width, self.has_num_cases)
+
if self.num_values >= 5000:
self.maf = 0.01
else:
@@ -547,12 +547,12 @@ def get_nearest_marker(this_trait, this_db):
return result[0][0]
-def get_table_widths(sample_groups, has_num_cases=False):
+def get_table_widths(sample_groups, sample_column_width, has_num_cases=False):
stats_table_width = 250
if len(sample_groups) > 1:
stats_table_width = 450
- trait_table_width = 380
+ trait_table_width = 300 + sample_column_width
if sample_groups[0].se_exists:
trait_table_width += 80
if has_num_cases:
--
cgit v1.2.3
From fbec8e8bb919cb866d70db9f93a942f4554395fb Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 16 Dec 2020 15:53:59 -0600
Subject: Removed unused JS and fixed mapping covariate selection to work for
both R/qtl and GEMMA
---
wqflask/wqflask/static/new/javascript/show_trait.js | 10 +---------
wqflask/wqflask/templates/show_trait_mapping_tools.html | 8 ++++----
2 files changed, 5 insertions(+), 13 deletions(-)
(limited to 'wqflask')
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 98f90f7d..9cd79687 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -100,15 +100,7 @@ d3.select("#select_compare_trait").on("click", (function(_this) {
return open_trait_selection();
};
})(this));
-d3.select("#select_covariates").on("click", (function(_this) {
- return function() {
- return open_covariate_selection();
- };
-})(this));
-$("#remove_covariates").click(function () {
- $("input[name=covariates]").val("")
- $(".selected-covariates").val("")
-});
+
$(".select_covariates").click(function () {
open_covariate_selection();
});
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index eca436c6..c42fe4aa 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -74,8 +74,8 @@
No collections available. Please add traits to a collection to use them as covariates.
{% else %}
-
-
+
+
{% endif %}
@@ -317,8 +317,8 @@
No collections available. Please add traits to a collection to use them as covariates.
{% else %}
--
cgit v1.2.3
From be1c1c1c48d75875f03b7ff4e91654f390571b58 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 17 Dec 2020 14:49:26 -0600
Subject: Added Mean (mean expression) column to phenotype correlation results
table
---
wqflask/wqflask/templates/correlation_page.html | 26 +++++++++++++++++--------
1 file changed, 18 insertions(+), 8 deletions(-)
(limited to 'wqflask')
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index 8e2a23fd..6188c0e7 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -95,14 +95,15 @@
{% elif target_dataset.type == 'Publish' %}
-
-
-
-
-
-
-
-
+
+
+
+
+
+
+
+
+
{% else %}
@@ -398,6 +399,13 @@
}
}
},
+ {
+ 'title': "Mean",
+ 'type': "natural-minus-na",
+ 'width': "40px",
+ 'data': "mean",
+ 'orderSequence': [ "desc", "asc"]
+ },
{
'title': "Authors",
'type': "natural",
@@ -514,6 +522,8 @@
} ],
{% if target_dataset.type == 'Geno' %}
"order": [[6, "asc" ]],
+ {% elif target_dataset.type == 'Publish' %}
+ "order": [[10, "asc" ]],
{% else %}
"order": [[9, "asc" ]],
{% endif %}
--
cgit v1.2.3
From 03de3751bd003117dce2bc4bf085092bd8f9a0fe Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 17 Dec 2020 14:50:34 -0600
Subject: Fixed some logic to work correctly with the changes to the way
correlation filters work + changed correlation python code to include Mean
(mean expression) for phenotype results
---
wqflask/wqflask/correlation/show_corr_results.py | 16 ++++++++++------
1 file changed, 10 insertions(+), 6 deletions(-)
(limited to 'wqflask')
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 7d3b9b9f..298a3559 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -71,7 +71,6 @@ class CorrelationResults(object):
assert('corr_sample_method' in start_vars)
assert('corr_samples_group' in start_vars)
assert('corr_dataset' in start_vars)
- #assert('min_expr' in start_vars)
assert('corr_return_results' in start_vars)
if 'loc_chr' in start_vars:
assert('min_loc_mb' in start_vars)
@@ -197,15 +196,15 @@ class CorrelationResults(object):
if (float(self.correlation_data[trait][0]) >= self.p_range_lower and
float(self.correlation_data[trait][0]) <= self.p_range_upper):
- if self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Geno":
-
+ if (self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Publish") and bool(trait_object.mean):
if (self.min_expr != None) and (float(trait_object.mean) < self.min_expr):
continue
- elif range_chr_as_int != None and (chr_as_int != range_chr_as_int):
+ if self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Geno":
+ if range_chr_as_int != None and (chr_as_int != range_chr_as_int):
continue
- elif (self.min_location_mb != None) and (float(trait_object.mb) < float(self.min_location_mb)):
+ if (self.min_location_mb != None) and (float(trait_object.mb) < float(self.min_location_mb)):
continue
- elif (self.max_location_mb != None) and (float(trait_object.mb) > float(self.max_location_mb)):
+ if (self.max_location_mb != None) and (float(trait_object.mb) > float(self.max_location_mb)):
continue
(trait_object.sample_r,
@@ -519,6 +518,7 @@ def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_ap
elif target_dataset.type == "Publish":
results_dict['abbreviation_display'] = "N/A"
results_dict['description'] = "N/A"
+ results_dict['mean'] = "N/A"
results_dict['authors_display'] = "N/A"
results_dict['additive'] = "N/A"
if for_api:
@@ -532,6 +532,8 @@ def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_ap
results_dict['abbreviation_display'] = trait.abbreviation
if bool(trait.description_display):
results_dict['description'] = trait.description_display
+ if bool(trait.mean):
+ results_dict['mean'] = f"{float(trait.mean):.3f}"
if bool(trait.authors):
authors_list = trait.authors.split(',')
if len(authors_list) > 6:
@@ -605,6 +607,7 @@ def get_header_fields(data_type, corr_method):
'Record',
'Abbreviation',
'Description',
+ 'Mean',
'Authors',
'Year',
'Sample rho',
@@ -618,6 +621,7 @@ def get_header_fields(data_type, corr_method):
'Record',
'Abbreviation',
'Description',
+ 'Mean',
'Authors',
'Year',
'Sample r',
--
cgit v1.2.3
From 47c15cdbd8d54afca05bf939dec8d7d461cff5a5 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 18 Dec 2020 14:30:13 -0600
Subject: Added function that fetches sample data and converts it to JSON to
show_trait.js
---
.../wqflask/static/new/javascript/show_trait.js | 23 ++++++++++++++++++++--
1 file changed, 21 insertions(+), 2 deletions(-)
(limited to 'wqflask')
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 98f90f7d..b71a9dd8 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -427,6 +427,25 @@ process_id = function() {
}
return processed;
};
+
+fetch_sample_values = function() {
+ // This is meant to fetch all sample values using DataTables API, since they can't all be submitted with the form when using Scroller (and this should also be faster)
+ sample_val_dict = {};
+
+ table = 'samples_primary';
+ if ($('#' + table).length){
+ table_api = $('#' + table).DataTable();
+ val_nodes = table_api.column(3).nodes().to$();
+ for (_j = 0; _j < val_nodes.length; _j++){
+ sample_name = val_nodes[_j].childNodes[0].name.split(":")[1]
+ sample_val = val_nodes[_j].childNodes[0].value
+ sample_val_dict[sample_name] = sample_val
+ }
+ }
+
+ return sample_val_dict;
+}
+
edit_data_change = function() {
var already_seen, checkbox, name, real_dict, real_value, real_variance, row, rows, sample_sets, table, tables, _i, _j, _len, _len1;
already_seen = {};
@@ -525,7 +544,7 @@ on_corr_method_change = function() {
$('select[name=corr_type]').change(on_corr_method_change);
submit_special = function(url) {
- get_table_contents_for_form_submit("trait_data_form");
+ $("input[name=sample_vals]").val(JSON.stringify(fetch_sample_values()))
$("#trait_data_form").attr("action", url);
$("#trait_data_form").submit();
};
@@ -549,7 +568,7 @@ get_table_contents_for_form_submit = function(form_id) {
});
}
-var corr_input_list = ['corr_type', 'primary_samples', 'trait_id', 'dataset', 'group', 'tool_used', 'form_url', 'corr_sample_method', 'corr_samples_group', 'corr_dataset', 'min_expr',
+var corr_input_list = ['sample_vals', 'corr_type', 'primary_samples', 'trait_id', 'dataset', 'group', 'tool_used', 'form_url', 'corr_sample_method', 'corr_samples_group', 'corr_dataset', 'min_expr',
'corr_return_results', 'loc_chr', 'min_loc_mb', 'max_loc_mb', 'p_range_lower', 'p_range_upper']
$(".corr_compute").on("click", (function(_this) {
--
cgit v1.2.3
From 66b8f70f162f2d6356c6e9af5066c5b90335f7c2 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 18 Dec 2020 14:33:04 -0600
Subject: Changed views.py to accept sample data for loading page and mapping
as JSON instead of having separate form parameters for each sample + removed
some commented out code/logging
---
wqflask/wqflask/views.py | 16 +++++-----------
1 file changed, 5 insertions(+), 11 deletions(-)
(limited to 'wqflask')
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 25563e86..c136711e 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -621,12 +621,13 @@ def loading_page():
wanted = initial_start_vars['wanted_inputs'].split(",")
start_vars = {}
for key, value in list(initial_start_vars.items()):
- if key in wanted or key.startswith(('value:')):
+ if key in wanted:
start_vars[key] = value
if 'n_samples' in start_vars:
n_samples = int(start_vars['n_samples'])
else:
+ sample_vals_dict = json.loads(start_vars['sample_vals'])
if 'group' in start_vars:
dataset = create_dataset(start_vars['dataset'], group_name = start_vars['group'])
else:
@@ -642,8 +643,7 @@ def loading_page():
samples = genofile_samples
for sample in samples:
- value = start_vars.get('value:' + sample)
- if value != "x":
+ if sample_vals_dict[sample] != "x":
n_samples += 1
start_vars['n_samples'] = n_samples
@@ -660,7 +660,6 @@ def loading_page():
@app.route("/run_mapping", methods=('POST',))
def mapping_results_page():
initial_start_vars = request.form
- #logger.debug("Mapping called with initial_start_vars:", initial_start_vars.items())
logger.info(request.url)
temp_uuid = initial_start_vars['temp_uuid']
wanted = (
@@ -670,6 +669,7 @@ def mapping_results_page():
'species',
'samples',
'vals',
+ 'sample_vals',
'first_run',
'output_files',
'geno_db_exists',
@@ -723,13 +723,11 @@ def mapping_results_page():
)
start_vars = {}
for key, value in list(initial_start_vars.items()):
- if key in wanted or key.startswith(('value:')):
+ if key in wanted:
start_vars[key] = value
- #logger.debug("Mapping called with start_vars:", start_vars)
version = "v3"
key = "mapping_results:{}:".format(version) + json.dumps(start_vars, sort_keys=True)
- #logger.info("key is:", pf(key))
with Bench("Loading cache"):
result = None # Just for testing
#result = Redis.get(key)
@@ -775,10 +773,6 @@ def mapping_results_page():
rendered_template = render_template("pair_scan_results.html", **result)
else:
gn1_template_vars = display_mapping_results.DisplayMappingResults(result).__dict__
- #pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL)
- #logger.info("pickled result length:", len(pickled_result))
- #Redis.set(key, pickled_result)
- #Redis.expire(key, 1*60)
with Bench("Rendering template"):
#if (gn1_template_vars['mapping_method'] == "gemma") or (gn1_template_vars['mapping_method'] == "plink"):
--
cgit v1.2.3
From 20314199985aa21a00a47f3c7b053ec49bc8b60d Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 18 Dec 2020 14:33:44 -0600
Subject: Added sample_vals input element that is meant to contain JSON for all
sample values (pulled from the sample table using DataTables API in
show_trait.js)
---
wqflask/wqflask/templates/show_trait.html | 1 +
1 file changed, 1 insertion(+)
(limited to 'wqflask')
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index c881eb76..77fc9342 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -35,6 +35,7 @@
+
--
cgit v1.2.3
From 969a421efc0bd4529607fdc14332acd897d8e106 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 18 Dec 2020 14:34:21 -0600
Subject: Added sample_vals to the list of mapping inputs that determines what
is included in start_vars when trait page parameters are passed to the
mapping loading page
---
wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
(limited to 'wqflask')
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 34582f21..3ae52975 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -141,7 +141,7 @@ $('input[name=display_all]').change((function(_this) {
})(this));
//ZS: This is a list of inputs to be passed to the loading page, since not all inputs on the trait page are relevant to mapping
-var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale',
+var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale', 'sample_vals',
'score_type', 'suggestive', 'significant', 'num_perm', 'permCheck', 'perm_output', 'perm_strata', 'categorical_vars', 'num_bootstrap', 'bootCheck', 'bootstrap_results',
'LRSCheck', 'covariates', 'maf', 'use_loco', 'manhattan_plot', 'control_marker', 'control_marker_db', 'do_control', 'genofile',
'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend', 'haplotypeAnalystCheck',
--
cgit v1.2.3
From 95d1887bba6b93ea310c226cb82e9cb64f75cc67 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 18 Dec 2020 14:35:09 -0600
Subject: Changed mapping_results.html to have a single sample_vals input
instead of separate ones for every sample + added sample_vals to the list of
inputs sent to the loading page
---
wqflask/wqflask/templates/mapping_results.html | 7 ++-----
1 file changed, 2 insertions(+), 5 deletions(-)
(limited to 'wqflask')
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 1a76ef7a..2fb37832 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -31,10 +31,7 @@
{% endif %}
-
- {% for sample in samples %}
-
- {% endfor %}
+
@@ -450,7 +447,7 @@
});
- var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale',
+ var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale', 'sample_vals',
'score_type', 'suggestive', 'significant', 'num_perm', 'permCheck', 'perm_output', 'perm_strata', 'categorical_vars', 'num_bootstrap', 'bootCheck', 'bootstrap_results',
'LRSCheck', 'covariates', 'maf', 'use_loco', 'manhattan_plot', 'color_scheme', 'manhattan_single_color', 'control_marker', 'control_marker_db', 'do_control', 'genofile',
'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend', 'haplotypeAnalystCheck',
--
cgit v1.2.3
From 7544d03a6d819d70779deb79d38b7465a648c1ff Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 18 Dec 2020 14:36:53 -0600
Subject: Changed run_mapping.py to get sample names and values from JSON
instead of a bunch of separate input parameters
---
wqflask/wqflask/marker_regression/run_mapping.py | 64 ++++++------------------
1 file changed, 15 insertions(+), 49 deletions(-)
(limited to 'wqflask')
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 891fcc66..a1f87b61 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -71,56 +71,22 @@ class RunMapping(object):
all_samples_ordered = self.dataset.group.all_samples_ordered()
self.vals = []
- if 'samples' in start_vars:
- self.samples = start_vars['samples'].split(",")
- if (len(genofile_samplelist) != 0):
- for sample in genofile_samplelist:
- if sample in self.samples:
- value = start_vars.get('value:' + sample)
- if value:
- self.vals.append(value)
- else:
- self.vals.append("x")
- else:
- for sample in self.samples:
- value = start_vars.get('value:' + sample)
- if value:
- self.vals.append(value)
+ self.samples = []
+ self.sample_vals = start_vars['sample_vals']
+ sample_val_dict = json.loads(self.sample_vals)
+ samples = sample_val_dict.keys()
+ if (len(genofile_samplelist) != 0):
+ for sample in genofile_samplelist:
+ self.samples.append(sample)
+ if sample in samples:
+ self.vals.append(sample_val_dict[sample])
+ else:
+ self.vals.append("x")
else:
- self.samples = []
- if (len(genofile_samplelist) != 0):
- for sample in genofile_samplelist:
- if sample in self.dataset.group.samplelist:
- in_trait_data = False
- for item in self.this_trait.data:
- if self.this_trait.data[item].name == sample:
- value = start_vars['value:' + self.this_trait.data[item].name]
- self.samples.append(self.this_trait.data[item].name)
- self.vals.append(value)
- in_trait_data = True
- break
- if not in_trait_data:
- value = start_vars.get('value:' + sample)
- if value:
- self.samples.append(sample)
- self.vals.append(value)
- else:
- self.vals.append("x")
- else:
- for sample in self.dataset.group.samplelist: # sample is actually the name of an individual
- in_trait_data = False
- for item in self.this_trait.data:
- if self.this_trait.data[item].name == sample:
- value = start_vars['value:' + self.this_trait.data[item].name]
- self.samples.append(self.this_trait.data[item].name)
- self.vals.append(value)
- in_trait_data = True
- break
- if not in_trait_data:
- value = start_vars.get('value:' + sample)
- if value:
- self.samples.append(sample)
- self.vals.append(value)
+ for sample in self.dataset.group.samplelist:
+ if sample in samples:
+ self.vals.append(sample_val_dict[sample])
+ self.samples.append(sample)
if 'n_samples' in start_vars:
self.n_samples = start_vars['n_samples']
--
cgit v1.2.3
From 6d493f7ef57322f226dd310497e4dc7518440cfd Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 18 Dec 2020 14:38:09 -0600
Subject: Changed display_mapping_results.py to get sample names and values
from the JSON sample_vals parameter
---
.../marker_regression/display_mapping_results.py | 19 +++++++++----------
1 file changed, 9 insertions(+), 10 deletions(-)
(limited to 'wqflask')
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 08c2d750..9f1b050d 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -270,8 +270,9 @@ class DisplayMappingResults(object):
# Needing for form submission when doing single chr
# mapping or remapping after changing options
- self.samples = start_vars['samples']
- self.vals = start_vars['vals']
+ self.sample_vals = start_vars['sample_vals']
+ self.sample_vals_dict = json.loads(self.sample_vals)
+
self.transform = start_vars['transform']
self.mapping_method = start_vars['mapping_method']
self.mapping_results_path = start_vars['mapping_results_path']
@@ -492,11 +493,10 @@ class DisplayMappingResults(object):
## count the amount of individuals to be plotted, and increase self.graphHeight
if self.haplotypeAnalystChecked and self.selectedChr > -1:
thisTrait = self.this_trait
- _strains, _vals, _vars, _aliases = thisTrait.export_informative()
smd=[]
- for ii, _val in enumerate(self.vals):
- if _val != "x":
- temp = GeneralObject(name=self.samples[ii], value=float(_val))
+ for sample in self.sample_vals_dict.keys():
+ if self.sample_vals_dict[sample] != "x":
+ temp = GeneralObject(name=sample, value=float(self.sample_vals_dict[sample]))
smd.append(temp)
else:
continue
@@ -1464,12 +1464,11 @@ class DisplayMappingResults(object):
yPaddingTop = yTopOffset
thisTrait = self.this_trait
- _strains, _vals, _vars, _aliases = thisTrait.export_informative()
smd=[]
- for ii, _val in enumerate(self.vals):
- if _val != "x":
- temp = GeneralObject(name=self.samples[ii], value=float(_val))
+ for sample in self.sample_vals_dict.keys():
+ if self.sample_vals_dict[sample] != "x":
+ temp = GeneralObject(name=sample, value=float(self.sample_vals_dict[sample]))
smd.append(temp)
else:
continue
--
cgit v1.2.3
From 41efd6840f2e1c052dbb77affd6f09fc2e2bcd05 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 18 Dec 2020 14:39:31 -0600
Subject: Changed show_corr_results.py to get sample names/values from the JSON
sample_vals parameter
---
wqflask/wqflask/correlation/show_corr_results.py | 12 +++++-------
1 file changed, 5 insertions(+), 7 deletions(-)
(limited to 'wqflask')
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 7d3b9b9f..be983c87 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -87,8 +87,6 @@ class CorrelationResults(object):
else:
helper_functions.get_species_dataset_trait(self, start_vars)
- #self.dataset.group.read_genotype_file()
-
corr_samples_group = start_vars['corr_samples_group']
self.sample_data = {}
@@ -454,13 +452,13 @@ class CorrelationResults(object):
if not excluded_samples:
excluded_samples = ()
+ sample_val_dict = json.loads(start_vars['sample_vals'])
for sample in sample_names:
if sample not in excluded_samples:
- # print("Looking for",sample,"in",start_vars)
- value = start_vars.get('value:' + sample)
- if value:
- if not value.strip().lower() == 'x':
- self.sample_data[str(sample)] = float(value)
+ value = sample_val_dict[sample]
+ if not value.strip().lower() == 'x':
+ self.sample_data[str(sample)] = float(value)
+
def do_bicor(this_trait_vals, target_trait_vals):
r_library = ro.r["library"] # Map the library function
--
cgit v1.2.3
From 453ac34383d54910e821609b80b69ff41c48d0ce Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 18 Dec 2020 14:53:01 -0600
Subject: Added Additive Effect when using LOCO with GEMMA
---
wqflask/wqflask/marker_regression/gemma_mapping.py | 11 ++++-------
1 file changed, 4 insertions(+), 7 deletions(-)
(limited to 'wqflask')
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 630a3afa..ab3a7278 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -54,7 +54,7 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf
TEMPDIR,
trait_filename)
if covariates != "":
- gemma_command += ' -c %s/%s_covariates.txt -a %s/%s_snps.txt -lmm 2 -maf %s > %s/gn2/%s.json' % (flat_files('mapping'),
+ gemma_command += ' -c %s/%s_covariates.txt -a %s/%s_snps.txt -lmm 9 -maf %s > %s/gn2/%s.json' % (flat_files('mapping'),
this_dataset.group.name,
flat_files('genotype/bimbam'),
genofile_name,
@@ -62,7 +62,7 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, maf
TEMPDIR,
gwa_output_filename)
else:
- gemma_command += ' -a %s/%s_snps.txt -lmm 2 -maf %s > %s/gn2/%s.json' % (flat_files('genotype/bimbam'),
+ gemma_command += ' -a %s/%s_snps.txt -lmm 9 -maf %s > %s/gn2/%s.json' % (flat_files('genotype/bimbam'),
genofile_name,
maf,
TEMPDIR,
@@ -184,11 +184,8 @@ def parse_loco_output(this_dataset, gwa_output_filename, loco="True"):
else:
marker['chr'] = line.split("\t")[0]
marker['Mb'] = float(line.split("\t")[2]) / 1000000
- if loco == "True":
- marker['p_value'] = float(line.split("\t")[9])
- else:
- marker['p_value'] = float(line.split("\t")[10])
- marker['additive'] = float(line.split("\t")[7])
+ marker['p_value'] = float(line.split("\t")[10])
+ marker['additive'] = float(line.split("\t")[7])
if math.isnan(marker['p_value']) or (marker['p_value'] <= 0):
marker['lod_score'] = 0
#marker['lrs_value'] = 0
--
cgit v1.2.3
From 69f92ef2bc10477a80eff96fb7cc83fee11f31e8 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 18 Dec 2020 17:05:55 -0600
Subject: This should fix the Github login error
---
wqflask/wqflask/user_login.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
(limited to 'wqflask')
diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py
index f25ebc32..b6266b2a 100644
--- a/wqflask/wqflask/user_login.py
+++ b/wqflask/wqflask/user_login.py
@@ -239,7 +239,7 @@ def github_oauth2():
}
result = requests.post("https://github.com/login/oauth/access_token", json=data)
- result_dict = {arr[0]:arr[1] for arr in [tok.split("=") for tok in [token.encode("utf-8") for token in result.text.split("&")]]}
+ result_dict = {arr[0]:arr[1] for arr in [tok.split("=") for tok in result.text.split("&")]}
github_user = get_github_user_details(result_dict["access_token"])
--
cgit v1.2.3
From fc717c36d334f364bbae8c98f31ddf78e18d64e3 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 18 Dec 2020 17:34:47 -0600
Subject: Added redirect_uri to the ORCID_AUTH_URL since it wasn't working due
to missing this parameter
---
wqflask/utility/tools.py | 2 +-
wqflask/wqflask/user_login.py | 6 ++++--
2 files changed, 5 insertions(+), 3 deletions(-)
(limited to 'wqflask')
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 68ef0f04..65df59c3 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -267,7 +267,7 @@ ORCID_CLIENT_SECRET = get_setting('ORCID_CLIENT_SECRET')
ORCID_AUTH_URL = None
if ORCID_CLIENT_ID != 'UNKNOWN' and ORCID_CLIENT_SECRET:
ORCID_AUTH_URL = "https://orcid.org/oauth/authorize?response_type=code&scope=/authenticate&show_login=true&client_id=" + \
- ORCID_CLIENT_ID+"&client_secret="+ORCID_CLIENT_SECRET
+ ORCID_CLIENT_ID+"&client_secret="+ORCID_CLIENT_SECRET + "&redirect_uri=" + GN2_BRANCH_URL + "n/login/orcid_oauth2"
ORCID_TOKEN_URL = get_setting('ORCID_TOKEN_URL')
ELASTICSEARCH_HOST = get_setting('ELASTICSEARCH_HOST')
diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py
index b6266b2a..bc608e84 100644
--- a/wqflask/wqflask/user_login.py
+++ b/wqflask/wqflask/user_login.py
@@ -25,7 +25,7 @@ from utility.logger import getLogger
logger = getLogger(__name__)
from smtplib import SMTP
-from utility.tools import SMTP_CONNECT, SMTP_USERNAME, SMTP_PASSWORD, LOG_SQL_ALCHEMY
+from utility.tools import SMTP_CONNECT, SMTP_USERNAME, SMTP_PASSWORD, LOG_SQL_ALCHEMY, GN2_BRANCH_URL
THREE_DAYS = 60 * 60 * 24 * 3
@@ -277,9 +277,11 @@ def orcid_oauth2():
data = {
"client_id": ORCID_CLIENT_ID,
"client_secret": ORCID_CLIENT_SECRET,
- "grant_type": "authorization_code",
+ "grant_type": "authorization_code",
+ "redirect_uri": GN2_BRANCH_URL + "n/login/orcid_oauth2",
"code": code
}
+
result = requests.post(ORCID_TOKEN_URL, data=data)
result_dict = json.loads(result.text.encode("utf-8"))
--
cgit v1.2.3
From 0560b297a9a6139079ee237bc8d98f471e7703f5 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 25 Dec 2020 19:18:48 -0600
Subject: Added edit_data_change to block_by_attribute_value so it will update
stats figures after using that tool
---
wqflask/wqflask/static/new/javascript/show_trait.js | 2 ++
1 file changed, 2 insertions(+)
(limited to 'wqflask')
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index e9c7cce1..312cc22f 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -641,6 +641,8 @@ block_by_attribute_value = function() {
this_val_node.value = "x";
}
}
+
+ edit_data_change();
};
$('#exclude_by_attr').click(block_by_attribute_value);
--
cgit v1.2.3
From c26304ed6a2937654794f908c13ccd3ba4a66453 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 28 Dec 2020 14:25:51 -0600
Subject: Fix issue that caused error bars to not work for bar chart
---
wqflask/wqflask/static/new/javascript/show_trait.js | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
(limited to 'wqflask')
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 312cc22f..6918cf34 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -448,7 +448,7 @@ edit_data_change = function() {
if (is_number(sample_val) && sample_val !== "") {
sample_val = parseFloat(sample_val);
sample_sets[table].add_value(sample_val);
- if (typeof var_nodes !== 'undefined'){
+ if (typeof var_nodes === 'undefined'){
sample_var = null;
} else {
sample_var = var_nodes[_j].childNodes[0].value
@@ -471,6 +471,7 @@ edit_data_change = function() {
}
}
}
+
}
update_stat_values(sample_sets);
--
cgit v1.2.3
From 3241a8de759f18bbbc73bd755419831db37e71a0 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 28 Dec 2020 15:01:31 -0600
Subject: Added 'Location Type' option to show_trait correlation options
---
wqflask/wqflask/templates/show_trait_calculate_correlations.html | 9 +++++++++
1 file changed, 9 insertions(+)
(limited to 'wqflask')
diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
index eaa0c308..46232b97 100644
--- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html
+++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
@@ -80,6 +80,15 @@
+
+
+
+
+
+
--
cgit v1.2.3
From ab9aebc567d1a10282ae55f282993a3fa9dd3582 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 28 Dec 2020 15:14:32 -0600
Subject: Changed correlation options to always show the location field and
both location_type options, since one or the other will always apply
---
wqflask/wqflask/templates/show_trait_calculate_correlations.html | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
(limited to 'wqflask')
diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
index 46232b97..cba977ac 100644
--- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html
+++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
@@ -84,12 +84,12 @@
-
+
--
cgit v1.2.3
From a336ca94fd473fdfd6cc5a83ce879429c0f1db92 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 28 Dec 2020 15:15:01 -0600
Subject: Added JS controlling which location_type options are available
depending upon the selected target dataset
---
wqflask/wqflask/static/new/javascript/show_trait.js | 11 ++++++++---
1 file changed, 8 insertions(+), 3 deletions(-)
(limited to 'wqflask')
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 6918cf34..a301615b 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -519,21 +519,26 @@ $('select[name=corr_type]').change(on_corr_method_change);
on_dataset_change = function() {
let dataset_type = $('select[name=corr_dataset] option:selected').data('type');
+ let location_type = $('select[name=location_type] option:selected').val();
if (dataset_type == "mrna_assay"){
$('#min_expr_filter').show();
- $('#location_filter').show();
+ $('select[name=location_type] option:disabled').prop('disabled', false)
}
else if (dataset_type == "pheno"){
$('#min_expr_filter').show();
- $('#location_filter').hide();
+ $('select[name=location_type]>option:eq(0)').prop('disabled', true).attr('selected', false);
+ $('select[name=location_type]>option:eq(1)').prop('disabled', false).attr('selected', true);
}
else {
$('#min_expr_filter').hide();
- $('#location_filter').show();
+ $('select[name=location_type]>option:eq(0)').prop('disabled', false).attr('selected', true);
+ $('select[name=location_type]>option:eq(1)').prop('disabled', true).attr('selected', false);
}
}
+
$('select[name=corr_dataset]').change(on_dataset_change);
+$('select[name=location_type]').change(on_dataset_change);
submit_special = function(url) {
get_table_contents_for_form_submit("trait_data_form");
--
cgit v1.2.3
From 8dd6f67d37c2d5cc800ee9dc33dd13a566e256fa Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 28 Dec 2020 15:48:50 -0600
Subject: Incorporated location_type into the filtering logic for the
correlation page
---
wqflask/wqflask/correlation/show_corr_results.py | 37 +++++++++++++++---------
1 file changed, 23 insertions(+), 14 deletions(-)
(limited to 'wqflask')
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 298a3559..6175dc7e 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -101,11 +101,12 @@ class CorrelationResults(object):
'min_loc_mb' in start_vars and
'max_loc_mb' in start_vars):
+ self.location_type = get_string(start_vars, 'location_type')
self.location_chr = get_string(start_vars, 'loc_chr')
self.min_location_mb = get_int(start_vars, 'min_loc_mb')
self.max_location_mb = get_int(start_vars, 'max_loc_mb')
else:
- self.location_chr = self.min_location_mb = self.max_location_mb = None
+ self.location_type = self.location_chr = self.min_location_mb = self.max_location_mb = None
self.get_formatted_corr_type()
self.return_number = int(start_vars['corr_return_results'])
@@ -173,23 +174,25 @@ class CorrelationResults(object):
self.correlation_data = collections.OrderedDict(sorted(list(self.correlation_data.items()),
key=lambda t: -abs(t[1][0])))
- if self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Geno":
- #ZS: Convert min/max chromosome to an int for the location range option
- range_chr_as_int = None
- for order_id, chr_info in list(self.dataset.species.chromosomes.chromosomes.items()):
- if 'loc_chr' in start_vars:
- if chr_info.name == self.location_chr:
- range_chr_as_int = order_id
+
+ #ZS: Convert min/max chromosome to an int for the location range option
+ range_chr_as_int = None
+ for order_id, chr_info in list(self.dataset.species.chromosomes.chromosomes.items()):
+ if 'loc_chr' in start_vars:
+ if chr_info.name == self.location_chr:
+ range_chr_as_int = order_id
for _trait_counter, trait in enumerate(list(self.correlation_data.keys())[:self.return_number]):
trait_object = create_trait(dataset=self.target_dataset, name=trait, get_qtl_info=True, get_sample_info=False)
if not trait_object:
continue
- if self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Geno":
- #ZS: Convert trait chromosome to an int for the location range option
- chr_as_int = 0
- for order_id, chr_info in list(self.dataset.species.chromosomes.chromosomes.items()):
+ chr_as_int = 0
+ for order_id, chr_info in list(self.dataset.species.chromosomes.chromosomes.items()):
+ if self.location_type == "highest_lod":
+ if chr_info.name == trait_object.locus_chr:
+ chr_as_int = order_id
+ else:
if chr_info.name == trait_object.chr:
chr_as_int = order_id
@@ -199,9 +202,15 @@ class CorrelationResults(object):
if (self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Publish") and bool(trait_object.mean):
if (self.min_expr != None) and (float(trait_object.mean) < self.min_expr):
continue
- if self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Geno":
- if range_chr_as_int != None and (chr_as_int != range_chr_as_int):
+
+ if range_chr_as_int != None and (chr_as_int != range_chr_as_int):
+ continue
+ if self.location_type == "highest_lod":
+ if (self.min_location_mb != None) and (float(trait_object.locus_mb) < float(self.min_location_mb)):
+ continue
+ if (self.max_location_mb != None) and (float(trait_object.locus_mb) > float(self.max_location_mb)):
continue
+ else:
if (self.min_location_mb != None) and (float(trait_object.mb) < float(self.min_location_mb)):
continue
if (self.max_location_mb != None) and (float(trait_object.mb) > float(self.max_location_mb)):
--
cgit v1.2.3
From dd2c510ea09ea3169cac3685b299640226d5606a Mon Sep 17 00:00:00 2001
From: Alexanderkabui
Date: Sun, 27 Dec 2020 23:17:36 +0300
Subject: update tests for run gemma
---
.../wqflask/marker_regression/test_gemma_mapping.py | 19 ++++++++++++-------
1 file changed, 12 insertions(+), 7 deletions(-)
(limited to 'wqflask')
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
index eab6afe6..fe2569b8 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_gemma_mapping.py
@@ -144,21 +144,26 @@ class TestGemmaMapping(unittest.TestCase):
"files": [["file_name", "user", "~/file1"],
["file_name", "user", "~/file2"]]
}
- return_file_1 = """X/Y\t L1\t21\tQ\tE\tA\tP\tMMB\tCDE\t0.5
-X/Y\tL2\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5
-chr\tL3\t12312\tQ\tE\tA\tP\tMMB\tCDE\t0.7"""
- return_file_2 = """chr\tother\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5"""
+ return_file="""X/Y\tM1\t28.457155\tQ\tE\tA\tMMB\t23.3\tW\t0.9\t0.85\t
+chr4\tM2\t12\tQ\tE\tMMB\tR\t24\tW\t0.87\t0.5
+Y\tM4\t12\tQ\tE\tMMB\tR\t11.6\tW\t0.21\t0.7
+X\tM5\t12\tQ\tE\tMMB\tR\t21.1\tW\t0.65\t0.6"""
+
+ return_file_2 = """chr\tother\t21322\tQ\tE\tA\tP\tMMB\tCDE\t0.5\t0.4"""
mock_os.path.isfile.return_value = True
file_to_write = """{"files":["file_1","file_2"]}"""
with mock.patch("builtins.open") as mock_open:
handles = (mock.mock_open(read_data="gwas").return_value, mock.mock_open(
- read_data=return_file_1).return_value, mock.mock_open(read_data=return_file_2).return_value)
+ read_data=return_file).return_value, mock.mock_open(read_data=return_file_2).return_value)
mock_open.side_effect = handles
results = parse_loco_output(
this_dataset={}, gwa_output_filename=".xw/")
- expected_results = [{'name': ' L1', 'chr': 'X/Y', 'Mb': 2.1e-05, 'p_value': 0.5, 'lod_score': 0.3010299956639812}, {
- 'name': 'L2', 'chr': 'X/Y', 'Mb': 0.021322, 'p_value': 0.5, 'lod_score': 0.3010299956639812}]
+ expected_results= [
+ {'name': 'M1', 'chr': 'X/Y', 'Mb': 2.8457155e-05, 'p_value': 0.85, 'additive': 23.3, 'lod_score': 0.07058107428570727},
+ {'name': 'M2', 'chr': 4, 'Mb': 1.2e-05, 'p_value': 0.5, 'additive': 24.0, 'lod_score': 0.3010299956639812},
+ {'name': 'M4', 'chr': 'Y', 'Mb': 1.2e-05, 'p_value': 0.7, 'additive': 11.6, 'lod_score': 0.1549019599857432},
+ {'name': 'M5', 'chr': 'X', 'Mb': 1.2e-05, 'p_value': 0.6, 'additive': 21.1, 'lod_score': 0.22184874961635637}]
self.assertEqual(expected_results, results)
--
cgit v1.2.3
From e7324bf55b7dcfd46f7a2ab52765977fb189c26b Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 29 Dec 2020 13:12:48 -0600
Subject: Added location_type to the list of inputs to correlation page (a list
of form inputs the correlation page needs is passed with it so it doesn't get
unrelated form inputs)
---
wqflask/wqflask/static/new/javascript/show_trait.js | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
(limited to 'wqflask')
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index a301615b..83d4f193 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -566,7 +566,7 @@ get_table_contents_for_form_submit = function(form_id) {
}
var corr_input_list = ['corr_type', 'primary_samples', 'trait_id', 'dataset', 'group', 'tool_used', 'form_url', 'corr_sample_method', 'corr_samples_group', 'corr_dataset', 'min_expr',
- 'corr_return_results', 'loc_chr', 'min_loc_mb', 'max_loc_mb', 'p_range_lower', 'p_range_upper']
+ 'corr_return_results', 'location_type', 'loc_chr', 'min_loc_mb', 'max_loc_mb', 'p_range_lower', 'p_range_upper']
$(".corr_compute").on("click", (function(_this) {
return function() {
--
cgit v1.2.3
From 1bd2d85624e04966ed20ec84dc6ba2cfda85d794 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 29 Dec 2020 15:03:22 -0600
Subject: Used a try/catch to deal with situations where there's no SE/var
column, since apparently var_nodes wasn't undefined, causing the previous
check to not work
---
wqflask/wqflask/static/new/javascript/show_trait.js | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
(limited to 'wqflask')
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 6918cf34..1025233b 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -448,15 +448,15 @@ edit_data_change = function() {
if (is_number(sample_val) && sample_val !== "") {
sample_val = parseFloat(sample_val);
sample_sets[table].add_value(sample_val);
- if (typeof var_nodes === 'undefined'){
- sample_var = null;
- } else {
+ try {
sample_var = var_nodes[_j].childNodes[0].value
if (is_number(sample_var)) {
sample_var = parseFloat(sample_var)
} else {
sample_var = null;
}
+ } catch {
+ sample_var = null;
}
sample_dict = {
value: sample_val,
--
cgit v1.2.3
From 7d8e41cd6d31c51adfedcf7abc0da553dd58762c Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 4 Jan 2021 13:04:55 -0600
Subject: Removed logging line from draw_probability_plot.js
---
wqflask/wqflask/static/new/javascript/draw_probability_plot.js | 1 -
1 file changed, 1 deletion(-)
(limited to 'wqflask')
diff --git a/wqflask/wqflask/static/new/javascript/draw_probability_plot.js b/wqflask/wqflask/static/new/javascript/draw_probability_plot.js
index 3d756303..1b944d4f 100644
--- a/wqflask/wqflask/static/new/javascript/draw_probability_plot.js
+++ b/wqflask/wqflask/static/new/javascript/draw_probability_plot.js
@@ -118,7 +118,6 @@
};
};
data = [make_data('samples_primary'), make_data('samples_other')];
- console.log("THE DATA IS:", data);
d3.select("#prob_plot_container svg").datum(data).call(chart);
if (js_data.trait_symbol != null) {
$("#prob_plot_title").html("