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authorGN22020-04-23 14:13:20 -0500
committerGN22020-04-23 14:13:20 -0500
commit6ce3ec06ffd9539ab4317f09f54564bd28b90087 (patch)
treeeea71f3dc2de4bb9cc6988dd5d72e51247b1f362
parentacb453007a355445f108932ba93032043376461c (diff)
parent79d935dfa02de7507103b45266a61264cfe8f735 (diff)
downloadgenenetwork2-6ce3ec06ffd9539ab4317f09f54564bd28b90087.tar.gz
Merge branch 'testing' of https://github.com/genenetwork/genenetwork2 into HEAD
-rw-r--r--wqflask/wqflask/marker_regression/display_mapping_results.py3
-rw-r--r--wqflask/wqflask/marker_regression/rqtl_mapping.py29
-rw-r--r--wqflask/wqflask/marker_regression/run_mapping.py9
-rw-r--r--wqflask/wqflask/static/new/javascript/show_trait.js2
-rw-r--r--wqflask/wqflask/templates/mapping_results.html22
-rw-r--r--wqflask/wqflask/user_login.py3
-rw-r--r--wqflask/wqflask/views.py20
7 files changed, 66 insertions, 22 deletions
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index a7e11738..2a53b60e 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -166,6 +166,7 @@ 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.transform = start_vars['transform']
self.mapping_method = start_vars['mapping_method']
self.mapping_results_path = start_vars['mapping_results_path']
if self.mapping_method == "rqtl_geno":
@@ -233,6 +234,8 @@ class DisplayMappingResults(object):
self.covariates = start_vars['covariates']
if 'maf' in start_vars.keys():
self.maf = start_vars['maf']
+ else:
+ self.maf = ""
if 'output_files' in start_vars.keys():
self.output_files = start_vars['output_files']
if 'use_loco' in start_vars.keys() and self.mapping_method == "gemma":
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index aae8e602..e1aa290b 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -36,7 +36,10 @@ def run_rqtl_geno(vals, samples, dataset, method, model, permCheck, num_perm, pe
generate_cross_from_geno(dataset)
GENOtoCSVR = ro.r["GENOtoCSVR"] # Map the local GENOtoCSVR function
crossfilelocation = TMPDIR + crossname + ".cross"
- genofilelocation = locate(dataset.group.genofile, "genotype")
+ if dataset.group.genofile:
+ genofilelocation = locate(dataset.group.genofile, "genotype")
+ else:
+ genofilelocation = locate(dataset.group.name + ".geno", "genotype")
cross_object = GENOtoCSVR(genofilelocation, crossfilelocation) # TODO: Add the SEX if that is available
if manhattan_plot:
@@ -91,9 +94,11 @@ def run_rqtl_geno(vals, samples, dataset, method, model, permCheck, num_perm, pe
perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", n_perm = num_perm, model=model, method=method)
perm_output, suggestive, significant = process_rqtl_perm_results(num_perm, perm_data_frame) # Functions that sets the thresholds for the webinterface
- return perm_output, suggestive, significant, process_rqtl_results(result_data_frame, dataset.group.species)
+ the_scale = check_mapping_scale(genofilelocation)
+ return perm_output, suggestive, significant, process_rqtl_results(result_data_frame, dataset.group.species), the_scale
else:
- return process_rqtl_results(result_data_frame, dataset.group.species)
+ the_scale = check_mapping_scale(genofilelocation)
+ return process_rqtl_results(result_data_frame, dataset.group.species), the_scale
def generate_cross_from_rdata(dataset):
rdata_location = locate(dataset.group.name + ".RData", "genotype/rdata")
@@ -286,4 +291,20 @@ def process_rqtl_results(result, species_name): # TODO: how to make this
marker['lod_score'] = output[i][2]
qtl_results.append(marker)
- return qtl_results \ No newline at end of file
+ return qtl_results
+
+def check_mapping_scale(genofile_location):
+ scale = "physic"
+ with open(genofile_location, "r") as geno_fh:
+ for line in geno_fh:
+ if line[0] == "@" or line[0] == "#":
+
+ if "@scale" in line:
+ scale = line.split(":")[1].strip()
+ break
+ else:
+ continue
+ else:
+ break
+
+ return scale \ No newline at end of file
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index e191902c..589be702 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -150,6 +150,10 @@ class RunMapping(object):
self.suggestive = ""
self.significant = ""
self.pair_scan = False # Initializing this since it is checked in views to determine which template to use
+ if 'transform' in start_vars:
+ self.transform = start_vars['transform']
+ else:
+ self.transform = ""
self.score_type = "LRS" #ZS: LRS or LOD
self.mapping_scale = "physic"
self.num_perm = 0
@@ -241,7 +245,6 @@ class RunMapping(object):
perm_strata = get_perm_strata(self.this_trait, primary_samples, self.categorical_vars, self.samples)
self.score_type = "LOD"
- #self.mapping_scale = "morgan"
self.control_marker = start_vars['control_marker']
self.do_control = start_vars['do_control']
if 'mapmethod_rqtl_geno' in start_vars:
@@ -252,9 +255,9 @@ class RunMapping(object):
#if start_vars['pair_scan'] == "true":
# self.pair_scan = True
if self.permCheck and self.num_perm > 0:
- self.perm_output, self.suggestive, self.significant, results = rqtl_mapping.run_rqtl_geno(self.vals, self.samples, self.dataset, self.method, self.model, self.permCheck, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.covariates)
+ self.perm_output, self.suggestive, self.significant, results, self.mapping_scale = rqtl_mapping.run_rqtl_geno(self.vals, self.samples, self.dataset, self.method, self.model, self.permCheck, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.covariates)
else:
- results = rqtl_mapping.run_rqtl_geno(self.vals, self.samples, self.dataset, self.method, self.model, self.permCheck, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.covariates)
+ results, self.mapping_scale = rqtl_mapping.run_rqtl_geno(self.vals, self.samples, self.dataset, self.method, self.model, self.permCheck, self.num_perm, perm_strata, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan, self.covariates)
elif self.mapping_method == "reaper":
if "startMb" in start_vars: #ZS: Check if first time page loaded, so it can default to ON
if "additiveCheck" in start_vars:
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 28d13345..d94a2347 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -367,6 +367,8 @@ make_table = function() {
var header, key, row, row_line, table, the_id, the_rows, value, _i, _len, _ref, _ref1;
if (js_data.trait_symbol != null) {
header = "<thead><tr><th style=\"color: white; background-color: #369; text-align: center;\" colspan=\"100%\">Trait " + js_data.trait_id + " - " + js_data.trait_symbol + "</th></tr><tr><th style=\"text-align: right; padding-left: 5px;\">Statistic</th>";
+ } else if (js_data.dataset_type == "Geno"){
+ header = "<thead><tr><th style=\"color: white; background-color: #369; text-align: center;\" colspan=\"100%\">Marker " + js_data.trait_id + "</th></tr><tr><th style=\"text-align: right; padding-left: 5px;\">Statistic</th>";
} else {
header = "<thead><tr><th style=\"color: white; background-color: #369; text-align: center;\" colspan=\"100%\">Trait " + js_data.trait_id + ": " + js_data.short_description + "</th></tr><tr><th style=\"text-align: right; padding-left: 5px;\">Statistic</th>";
}
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index ba0ebef9..7e05be18 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -36,7 +36,7 @@
<input type="hidden" name="value:{{ sample }}" value="{{ vals[loop.index - 1] }}">
{% endfor %}
<input type="hidden" name="num_vals" value="{{ n_samples }}">
- <input type="hidden" name="maf">
+ <input type="hidden" name="maf" value="{{ maf }}">
<input type="hidden" name="use_loco" value="{{ use_loco }}">
<input type="hidden" name="selected_chr" value="{{ selectedChr }}">
<input type="hidden" name="manhattan_plot" value="{{ manhattan_plot }}">
@@ -45,10 +45,14 @@
<input type="hidden" name="num_bootstrap" value="{{ nboot }}">
<input type="hidden" name="do_control" value="{{ doControl }}">
<input type="hidden" name="control_marker" value="{{ controlLocus }}">
- <input type="hidden" name="covariates" values="{{ covariates }}">
+ <input type="hidden" name="covariates" value="{{ covariates }}">
<input type="hidden" name="mapmethod_rqtl_geno" value="{{ mapmethod_rqtl_geno }}">
<input type="hidden" name="mapmodel_rqtl_geno" value="{{ mapmodel_rqtl_geno }}">
<input type="hidden" name="pair_scan" value="{{ pair_scan }}">
+ <input type="hidden" name="transform" value="{{ transform }}">
+ <input type="hidden" name="tool_used" value="Mapping">
+ <input type="hidden" name="wanted_inputs" value="">
+ <input type="hidden" name="form_url" value="/run_mapping">
<div class="container">
<div class="col-xs-5">
@@ -422,11 +426,19 @@
});
+ var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale',
+ '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',
+ 'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', 'group', 'species', 'reaper_version', 'primary_samples', 'num_vals']
+
+ $('input[name=wanted_inputs]').val(mapping_input_list.join(","));
+
chrView = function(this_chr, chr_mb_list) {
$('input[name=selected_chr]').val(this_chr)
$('input[name=chr_mb_list]').val(chr_mb_list)
- $('#marker_regression_form').attr('action', '/run_mapping');
+ $('#marker_regression_form').attr('action', '/loading');
return $('#marker_regression_form').submit();
};
@@ -436,13 +448,13 @@
$('input[name=endMb]').val(end_mb)
//$('input[name=mb_range]').val(start_mb + "," + end_mb)
- $('#marker_regression_form').attr('action', '/run_mapping');
+ $('#marker_regression_form').attr('action', '/loading');
return $('#marker_regression_form').submit();
};
remap = function() {
$('input[name=selected_chr]').val($('select[name=chromosomes]').val());
- $('#marker_regression_form').attr('action', '/run_mapping');
+ $('#marker_regression_form').attr('action', '/loading');
return $('#marker_regression_form').submit();
};
diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py
index 40d9925c..edd272c2 100644
--- a/wqflask/wqflask/user_login.py
+++ b/wqflask/wqflask/user_login.py
@@ -42,9 +42,6 @@ def basic_info():
user_agent = request.headers.get('User-Agent'))
def encode_password(pass_gen_fields, unencrypted_password):
- logger.debug("THE TYPE:", type(pass_gen_fields))
- logger.debug("pass_gen_fields:", pass_gen_fields)
- logger.debug("hashfunc:", pass_gen_fields['hashfunc'])
hashfunc = getattr(hashlib, pass_gen_fields['hashfunc'])
salt = base64.b64decode(pass_gen_fields['salt'])
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 76857650..e351a2d4 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -583,18 +583,23 @@ def loading_page():
if key in wanted or key.startswith(('value:')):
start_vars[key] = value
- if 'primary_samples' in start_vars:
- samples = start_vars['primary_samples'].split(",")
- for sample in samples:
- value = start_vars.get('value:' + sample)
- if value != "x":
- num_vals += 1
+ if 'num_vals' in start_vars:
+ num_vals = int(start_vars['num_vals'])
+ else:
+ if 'primary_samples' in start_vars:
+ samples = start_vars['primary_samples'].split(",")
+ for sample in samples:
+ value = start_vars.get('value:' + sample)
+ if value != "x":
+ num_vals += 1
start_vars['num_vals'] = num_vals
+ start_vars['wanted_inputs'] = initial_start_vars['wanted_inputs']
start_vars_container['start_vars'] = start_vars
else:
start_vars_container['start_vars'] = initial_start_vars
+
rendered_template = render_template("loading.html", **start_vars_container)
return rendered_template
@@ -658,7 +663,8 @@ def mapping_results_page():
'mapmodel_rqtl_geno',
'temp_trait',
'reaper_version',
- 'num_vals'
+ 'num_vals',
+ 'transform'
)
start_vars = {}
for key, value in initial_start_vars.iteritems():