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-rwxr-xr-xwqflask/wqflask/marker_regression/marker_regression.py7
-rwxr-xr-xwqflask/wqflask/show_trait/show_trait.py25
-rwxr-xr-xwqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js1
-rwxr-xr-xwqflask/wqflask/templates/index_page.html2
-rwxr-xr-xwqflask/wqflask/templates/show_trait_details.html12
-rwxr-xr-xwqflask/wqflask/templates/show_trait_mapping_tools.html54
-rwxr-xr-xwqflask/wqflask/views.py1
7 files changed, 65 insertions, 37 deletions
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 757aeb72..b33efc1f 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -91,6 +91,7 @@ class MarkerRegression(object):
else:
self.num_perm = start_vars['num_perm']
self.control = start_vars['control_marker']
+ self.do_control = start_vars['do_control']
print("StartVars:", start_vars)
self.method = start_vars['mapmethod_rqtl_geno']
self.model = start_vars['mapmodel_rqtl_geno']
@@ -352,7 +353,7 @@ class MarkerRegression(object):
covar = self.create_covariates(cross_object) # Create the additive covariate matrix
if self.pair_scan:
- if(r_sum(covar)[0] > 0): # If sum(covar) > 0 we have a covariate matrix
+ if self.do_control == "true": # If sum(covar) > 0 we have a covariate matrix
print("Using covariate"); result_data_frame = scantwo(cross_object, pheno = "the_pheno", addcovar = covar, model=self.model, method=self.method, n_cluster = 16)
else:
print("No covariates"); result_data_frame = scantwo(cross_object, pheno = "the_pheno", model=self.model, method=self.method, n_cluster = 16)
@@ -367,13 +368,13 @@ class MarkerRegression(object):
return self.process_pair_scan_results(result_data_frame)
else:
- if(r_sum(covar)[0] > 0):
+ if self.do_control == "true":
print("Using covariate"); result_data_frame = scanone(cross_object, pheno = "the_pheno", addcovar = covar, model=self.model, method=self.method)
else:
print("No covariates"); result_data_frame = scanone(cross_object, pheno = "the_pheno", model=self.model, method=self.method)
if int(self.num_perm) > 0: # Do permutation (if requested by user)
- if(r_sum(covar)[0] > 0):
+ if self.do_control == "true":
perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", addcovar = covar, n_perm = int(self.num_perm), model=self.model, method=self.method)
else:
perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", n_perm = int(self.num_perm), model=self.model, method=self.method)
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 871d1880..e83437ab 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -102,11 +102,13 @@ class ShowTrait(object):
print("self.dataset.type:", self.dataset.type)
if hasattr(self.this_trait, 'locus_chr') and self.this_trait.locus_chr != "" and self.dataset.type != "Geno" and self.dataset.type != "Publish":
- self.nearest_marker1 = get_nearest_marker(self.this_trait, self.dataset)[0]
- self.nearest_marker2 = get_nearest_marker(self.this_trait, self.dataset)[1]
+ self.nearest_marker = get_nearest_marker(self.this_trait, self.dataset)
+ #self.nearest_marker1 = get_nearest_marker(self.this_trait, self.dataset)[0]
+ #self.nearest_marker2 = get_nearest_marker(self.this_trait, self.dataset)[1]
else:
- self.nearest_marker1 = ""
- self.nearest_marker2 = ""
+ self.nearest_marker = ""
+ #self.nearest_marker1 = ""
+ #self.nearest_marker2 = ""
self.make_sample_lists(self.this_trait)
@@ -120,11 +122,13 @@ class ShowTrait(object):
hddn['mapping_display_all'] = True
hddn['suggestive'] = 0
hddn['num_perm'] = 0
- hddn['manhattan_plot'] = False
+ hddn['manhattan_plot'] = ""
if hasattr(self.this_trait, 'locus_chr') and self.this_trait.locus_chr != "" and self.dataset.type != "Geno" and self.dataset.type != "Publish":
- hddn['control_marker'] = self.nearest_marker1+","+self.nearest_marker2
+ hddn['control_marker'] = self.nearest_marker
+ #hddn['control_marker'] = self.nearest_marker1+","+self.nearest_marker2
else:
hddn['control_marker'] = ""
+ hddn['do_control'] = False
hddn['maf'] = 0.01
hddn['compare_traits'] = []
hddn['export_data'] = ""
@@ -1231,21 +1235,24 @@ def get_nearest_marker(this_trait, this_db):
print("this_chr:", this_chr)
this_mb = this_trait.locus_mb
print("this_mb:", this_mb)
+ #One option is to take flanking markers, another is to take the two (or one) closest
query = """SELECT Geno.Name
FROM Geno, GenoXRef, GenoFreeze
WHERE Geno.Chr = '{}' AND
GenoXRef.GenoId = Geno.Id AND
GenoFreeze.Id = GenoXRef.GenoFreezeId AND
GenoFreeze.Name = '{}'
- ORDER BY ABS( Geno.Mb - {}) LIMIT 2""".format(this_chr, this_db.group.name+"Geno", this_mb)
+ ORDER BY ABS( Geno.Mb - {}) LIMIT 1""".format(this_chr, this_db.group.name+"Geno", this_mb)
print("query:", query)
result = g.db.execute(query).fetchall()
print("result:", result)
if result == []:
- return "", ""
+ return ""
+ #return "", ""
else:
- return result[0][0], result[1][0]
+ return result[0][0]
+ #return result[0][0], result[1][0]
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 3be40a57..2f26d6cb 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -185,6 +185,7 @@
$('input[name=num_perm]').val($('input[name=num_perm_rqtl_geno]').val());
$('input[name=manhattan_plot]').val($('input[name=manhattan_plot_rqtl]:checked').val());
$('input[name=control_marker]').val($('input[name=control_rqtl_geno]').val());
+ $('input[name=do_control]').val($('input[name=do_control_rqtl]:checked').val());
form_data = $('#trait_data_form').serialize();
console.log("form_data is:", form_data);
return do_ajax_post(url, form_data);
diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html
index 2bbfcd91..6c630344 100755
--- a/wqflask/wqflask/templates/index_page.html
+++ b/wqflask/wqflask/templates/index_page.html
@@ -271,7 +271,7 @@
// Has the enter key been pressed?
if ( (window.event ? event.keyCode : e.which) == 13) {
// If it has been so, manually submit the <form>
- document.forms[0].submit();
+ document.forms[1].submit();
}
}
</script>
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 3259d349..cdaa919e 100755
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -38,12 +38,6 @@
<dt>Resource Links</dt>
{% if this_trait.dataset.type == 'ProbeSet' %}
<dd>
- {% if this_trait.symbol != None %}
- <a href="http://www.genotation.org/Getd2g.pl?gene_list={{ this_trait.symbol }}" target="_blank" title="Related descriptive, genomic, clinical, functional and drug-therapy information">
- Genotation
- </a>
- &nbsp;&nbsp;
- {% endif %}
{% if this_trait.geneid != None %}
<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids={{ this_trait.geneid }}" target="_blank" title="Info from NCBI Entrez Gene">
Gene
@@ -62,6 +56,12 @@
</a>
&nbsp;&nbsp;
{% endif %}
+ {% if this_trait.symbol != None %}
+ <a href="http://www.genotation.org/Getd2g.pl?gene_list={{ this_trait.symbol }}" target="_blank" title="Related descriptive, genomic, clinical, functional and drug-therapy information">
+ Genotation
+ </a>
+ &nbsp;&nbsp;
+ {% endif %}
</dd>
{% endif %}
</dl>
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 7f26a252..de25f4ee 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -1,6 +1,6 @@
<div>
{% if (use_pylmm_rqtl and dataset.group.species != "human") or use_plink_gemma %}
- <div class="col-xs-6">
+ <div class="col-xs-4">
<div class="tabbable"> <!-- Only required for left/right tabs -->
<ul class="nav nav-pills">
@@ -31,9 +31,9 @@
<div class="tab-content">
{% if use_pylmm_rqtl and not use_plink_gemma and dataset.group.species != "human" %}
<div class="tab-pane active" id="pylmm">
- <div style="padding: 20px" class="form-horizontal">
+ <div style="margin-top: 20px" class="form-horizontal">
<div class="mapping_method_fields form-group">
- <label for="mapping_permutations" class="col-xs-2 control-label">Permutations</label>
+ <label for="mapping_permutations" class="col-xs-3 control-label">Permutations</label>
<div style="margin-left: 20px;" class="col-xs-4 controls">
<input name="num_perm_pylmm" value="" type="text" class="form-control">
</div>
@@ -41,16 +41,26 @@
<div id="permutations_alert" class="alert alert-error alert-warning" style="display:none;">
Please be aware that permutations can take a very long time (~20 minutes for 500 permutations)
</div>
+<!--
<div class="mapping_method_fields form-group">
- <label for="control_for" class="col-xs-2 control-label">Control&nbsp;for</label>
+ <label for="control_for" class="col-xs-3 control-label">Control&nbsp;for</label>
<div style="margin-left: 20px;" class="col-xs-4 controls">
{% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %}
- <input name="control_pylmm" value="{{ nearest_marker1+","+nearest_marker2 }}" type="text" />
+ <input name="control_pylmm" value="{{ nearest_marker }}" type="text" />
{% else %}
<input name="control_pylmm" value="" type="text" />
{% endif %}
+ <label class="radio-inline">
+ <input type="radio" name="do_control_pylmm" value="true">
+ Yes
+ </label>
+ <label class="radio-inline">
+ <input type="radio" name="do_control_pylmm" value="false" checked="">
+ No
+ </label>
</div>
</div>
+-->
<div class="mapping_method_fields form-group">
<label style="text-align:left;" class="col-xs-12 control-label">Manhattan Plot</label>
@@ -68,7 +78,7 @@
<div class="form-group">
<div style="padding-left:15px;" class="controls">
<button id="pylmm_compute" class="btn submit_special btn-primary" title="Compute Marker Regression">
- <i class="icon-ok-circle icon-white"></i> Open Mapping Tool
+ <i class="icon-ok-circle icon-white"></i> Compute
</button>
</div>
</div>
@@ -76,29 +86,37 @@
</div>
<div class="tab-pane" id="rqtl_geno">
- <div style="padding: 20px" class="form-horizontal">
+ <div style="margin-top: 20px" class="form-horizontal">
<div class="mapping_method_fields form-group">
- <label for="mapping_permutations" class="col-xs-2 control-label">Permutations</label>
+ <label for="mapping_permutations" class="col-xs-3 control-label">Permutations</label>
<div style="margin-left: 20px;" class="col-xs-4 controls">
- <input name="num_perm_rqtl_geno" value="2000" type="text" class="form-control">
+ <input name="num_perm_rqtl_geno" value="" type="text" class="form-control">
</div>
</div>
<div id="permutations_alert" class="alert alert-error alert-warning" style="display:none;">
Please be aware that permutations can take a very long time (~20 minutes for 500 permutations)
</div>
<div class="mapping_method_fields form-group">
- <label for="control_for" class="col-xs-2 control-label">Control&nbsp;for</label>
+ <label for="control_for" class="col-xs-3 control-label">Control&nbsp;for</label>
<div style="margin-left: 20px;" class="col-xs-4 controls">
{% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %}
- <input name="control_rqtl_geno" value="{{ nearest_marker1+","+nearest_marker2 }}" type="text" style="width: 160px;" class="form-control" />
+ <input name="control_rqtl_geno" value="{{ nearest_marker }}" type="text" style="width: 160px;" class="form-control" />
{% else %}
<input name="control_rqtl_geno" value="" type="text" class="form-control" />
{% endif %}
+ <label class="radio-inline">
+ <input type="radio" name="do_control_rqtl" value="true">
+ Yes
+ </label>
+ <label class="radio-inline">
+ <input type="radio" name="do_control_rqtl" value="false" checked="">
+ No
+ </label>
</div>
</div>
<div class="mapping_method_fields form-group">
- <label for="mapmethod_rqtl_geno" style="text-align:left;" class="col-xs-2 control-label">Method</label>
+ <label for="mapmethod_rqtl_geno" style="text-align:left;" class="col-xs-3 control-label">Method</label>
<div class="col-xs-4 controls">
<select name="mapmethod_rqtl_geno" class="form-control">
<option value="em">em</option>
@@ -113,7 +131,7 @@
</div>
<div class="mapping_method_fields form-group">
- <label for="mapmodel_rqtl_geno" style="text-align:left;" class="col-xs-2 control-label">Model</label>
+ <label for="mapmodel_rqtl_geno" style="text-align:left;" class="col-xs-3 control-label">Model</label>
<div class="col-xs-4 controls">
<select name="mapmodel_rqtl_geno" class="form-control">
<option value="normal">normal</option>
@@ -155,23 +173,23 @@
<div class="form-group">
<div style="padding-left:15px;" class="controls">
<button id="rqtl_geno_compute" class="btn submit_special btn-primary" data-url="/marker_regression" title="Compute Marker Regression">
- <i class="icon-ok-circle icon-white"></i> Open Mapping Tool
+ <i class="icon-ok-circle icon-white"></i> Compute
</button>
</div>
</div>
</div>
</div>
<div class="tab-pane" id="interval_mapping">
- <div style="padding: 20px" class="form-horizontal">
+ <div style="margin-top: 20px" class="form-horizontal">
<div class="mapping_method_fields form-group">
- <label for="mapping_permutations" class="col-xs-2 control-label">Permutations</label>
+ <label for="mapping_permutations" class="col-xs-3 control-label">Permutations</label>
<div style="margin-left: 20px;" class="col-xs-4 controls">
<input name="num_perm_reaper" value="2000" type="text" class="form-control">
</div>
</div>
<!--
<div class="mapping_method_fields form-group">
- <label for="mapping_bootstraps" class="col-xs-2 control-label" title="Bootstrapping Resamples">Bootstrap</label>
+ <label for="mapping_bootstraps" class="col-xs-3 control-label" title="Bootstrapping Resamples">Bootstrap</label>
<div style="margin-left: 20px;" class="col-xs-4 controls">
<input name="mapping_bootstraps" value="2000" type="text" class="form-control">
</div>
@@ -208,7 +226,7 @@
<div class="form-group">
<div style="padding-left:15px;" class="controls">
<button id="interval_mapping_compute" class="btn submit_special btn-primary" data-url="/interval_mapping" title="Compute Interval Mapping">
- <i class="icon-ok-circle icon-white"></i> Open Mapping Tool
+ <i class="icon-ok-circle icon-white"></i> Compute
</button>
</div>
</div>
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 00c8d00d..3cff9a0c 100755
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -318,6 +318,7 @@ def marker_regression_page():
'manhattan_plot',
'control_marker',
'control_marker_db',
+ 'do_control',
'pair_scan',
'mapmethod_rqtl_geno',
'mapmodel_rqtl_geno'
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 12:28:36 +0000