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-rwxr-xr-xwqflask/wqflask/interval_mapping/interval_mapping.py196
-rwxr-xr-xwqflask/wqflask/marker_regression/marker_regression.py75
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression_gn1.py18
-rwxr-xr-xwqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js4
-rw-r--r--wqflask/wqflask/templates/marker_regression_gn1.html5
-rwxr-xr-xwqflask/wqflask/templates/show_trait_mapping_tools.html18
-rwxr-xr-xwqflask/wqflask/views.py44
7 files changed, 135 insertions, 225 deletions
diff --git a/wqflask/wqflask/interval_mapping/interval_mapping.py b/wqflask/wqflask/interval_mapping/interval_mapping.py
index 46aac86c..e8ac99d7 100755
--- a/wqflask/wqflask/interval_mapping/interval_mapping.py
+++ b/wqflask/wqflask/interval_mapping/interval_mapping.py
@@ -58,7 +58,7 @@ class IntervalMapping(object):
self.json_data = {}
self.json_data['lodnames'] = ['lod.hk']
- self.gen_reaper_results(tempdata)
+ self.gen_reaper_results()
#Get chromosome lengths for drawing the interval map plot
chromosome_mb_lengths = {}
@@ -102,76 +102,8 @@ class IntervalMapping(object):
else:
self.control_locus = None
- def gen_qtl_results(self, tempdata):
- """Generates qtl results for plotting interval map"""
- self.dataset.group.get_markers()
- genotype = self.dataset.group.read_genotype_file()
-
- samples, values, variances = self.this_trait.export_informative()
-
- trimmed_samples = []
- trimmed_values = []
- for i in range(0, len(samples)):
- if samples[i] in self.dataset.group.samplelist:
- trimmed_samples.append(samples[i])
- trimmed_values.append(values[i])
-
- #if self.weighted_regression:
- # self.lrs_array = self.genotype.permutation(strains = trimmed_samples,
- # trait = trimmed_values,
- # variance = variances,
- # nperm=self.num_permutations)
- #else:
- self.lrs_array = genotype.permutation(strains = trimmed_samples,
- trait = trimmed_values,
- nperm= self.num_permutations)
- self.suggestive = self.lrs_array[int(self.num_permutations*0.37-1)]
- self.significant = self.lrs_array[int(self.num_permutations*0.95-1)]
-
- print("samples:", trimmed_samples)
-
- if self.control_locus:
- #if self.weighted_regression:
- # self.qtl_results = self.dataset.genotype.regression(strains = samples,
- # trait = values,
- # variance = variances,
- # control = self.control_locus)
- #else:
- reaper_results = genotype.regression(strains = trimmed_samples,
- trait = trimmed_values,
- control = self.control_locus)
- else:
- #if self.weighted_regression:
- # self.qtl_results = self.dataset.genotype.regression(strains = samples,
- # trait = values,
- # variance = variances)
- #else:
- print("strains:", trimmed_samples)
- print("trait:", trimmed_values)
- reaper_results = genotype.regression(strains = trimmed_samples,
- trait = trimmed_values)
-
- #Need to convert the QTL objects that qtl reaper returns into a json serializable dictionary
- self.qtl_results = []
- self.json_data['chr'] = []
- self.json_data['pos'] = []
- self.json_data['lod.hk'] = []
- self.json_data['markernames'] = []
- for qtl in reaper_results:
- reaper_locus = qtl.locus
- self.json_data['pos'].append(reaper_locus.Mb)
- self.json_data['lod.hk'].append(qtl.lrs)
- self.json_data['markernames'].append(reaper_locus.name)
- if self.additive:
- self.json_data['additive'] = []
- self.json_data['additive'].append(qtl.additive)
- locus = {"name":reaper_locus.name, "chr":reaper_locus.chr, "cM":reaper_locus.cM, "Mb":reaper_locus.Mb}
- qtl = {"lrs": qtl.lrs, "locus": locus, "additive": qtl.additive}
- self.qtl_results.append(qtl)
-
-
- def gen_reaper_results(self, tempdata):
+ def gen_reaper_results(self):
genotype = self.dataset.group.read_genotype_file()
samples, values, variances = self.this_trait.export_informative()
@@ -249,127 +181,3 @@ class IntervalMapping(object):
trimmed_genotype_data.append(new_genotypes)
return trimmed_genotype_data
- #def get_qtl_results(self):
- # """Gets the LOD (or LRS) score at each marker in order do the qtl mapping"""
- #
- #
- #
- # #self.genotype = self.genotype.addinterval()
- # #resultSlice = []
- # #controlGeno = []
- #
- # #if self.multipleInterval:
- # # self.suggestive = 0
- # # self.significance = 0
- # # if self.selectedChr > -1:
- # # self.genotype.chromosome = [self.genotype[self.selectedChr]]
- # #else:
- # #single interval mapping
- # #try:
- # # self.suggestive = float(fd.formdata.getvalue('permSuggestive'))
- # # self.significance = float(fd.formdata.getvalue('permSignificance'))
- # #except:
- # # self.suggestive = None
- # # self.significance = None
- #
- # #NOT DOING MULTIPLE TRAITS YET, BUT WILL NEED TO LATER
- # #_strains, _vals, _vars = self.traitList[0].exportInformative(weightedRegression)
- #
- # #if webqtlUtil.ListNotNull(_vars):
- # # pass
- # #else:
- # # weightedRegression = 0
- # # _strains, _vals, _vars = self.traitList[0].exportInformative()
- #
- # ##locate genotype of control Locus
- # #if self.controlLocus:
- # # controlGeno2 = []
- # # _FIND = 0
- # # for _chr in self.genotype:
- # # for _locus in _chr:
- # # if _locus.name == self.controlLocus:
- # # controlGeno2 = _locus.genotype
- # # _FIND = 1
- # # break
- # # if _FIND:
- # # break
- # # if controlGeno2:
- # # _prgy = list(self.genotype.prgy)
- # # for _strain in _strains:
- # # _idx = _prgy.index(_strain)
- # # controlGeno.append(controlGeno2[_idx])
- # # else:
- # # return "The control marker you selected is not in the genofile."
- # #
- # #
- # # if self.significance and self.suggestive:
- # # pass
- # # else:
- # # if self.permChecked:
- # # if weightedRegression:
- # # self.LRSArray = self.genotype.permutation(strains = _strains, trait = _vals,
- # # variance = _vars, nperm=fd.nperm)
- # # else:
- # # self.LRSArray = self.genotype.permutation(strains = _strains, trait = _vals,
- # # nperm=fd.nperm)
- # # self.suggestive = self.LRSArray[int(fd.nperm*0.37-1)]
- # # self.significance = self.LRSArray[int(fd.nperm*0.95-1)]
- # #
- # # else:
- # # self.suggestive = 9.2
- # # self.significance = 16.1
- # #
- # # #calculating bootstrap
- # # #from now on, genotype could only contain a single chromosome
- # # #permutation need to be performed genome wide, this is not the case for bootstrap
- # #
- # # #due to the design of qtlreaper, composite regression need to be performed genome wide
- # # if not self.controlLocus and self.selectedChr > -1:
- # # self.genotype.chromosome = [self.genotype[self.selectedChr]]
- # # elif self.selectedChr > -1: #self.controlLocus and self.selectedChr > -1
- # # lociPerChr = map(len, self.genotype)
- # # resultSlice = reduce(lambda X, Y: X+Y, lociPerChr[:self.selectedChr], 0)
- # # resultSlice = [resultSlice,resultSlice+lociPerChr[self.selectedChr]]
- # # else:
- # # pass
- #
- # #calculate QTL for each trait
- # self.qtl_results = []
- #
- # #for thisTrait in self.traitList:
- # _strains, _vals, _vars = thisTrait.exportInformative(weightedRegression)
- # if self.controlLocus:
- # if weightedRegression:
- # qtlresult = self.genotype.regression(strains = _strains, trait = _vals,
- # variance = _vars, control = self.controlLocus)
- # else:
- # qtlresult = self.genotype.regression(strains = _strains, trait = _vals,
- # control = self.controlLocus)
- # if resultSlice:
- # qtlresult = qtlresult[resultSlice[0]:resultSlice[1]]
- # else:
- # if weightedRegression:
- # qtlresult = self.genotype.regression(strains = _strains, trait = _vals,
- # variance = _vars)
- # else:
- # qtlresult = self.genotype.regression(strains = _strains, trait = _vals)
- #
- # self.qtlresults.append(qtlresult)
- #
- # if not self.multipleInterval:
- # if self.controlLocus and self.selectedChr > -1:
- # self.genotype.chromosome = [self.genotype[self.selectedChr]]
- #
- # if self.bootChecked:
- # if controlGeno:
- # self.bootResult = self.genotype.bootstrap(strains = _strains, trait = _vals,
- # control = controlGeno, nboot=fd.nboot)
- # elif weightedRegression:
- # self.bootResult = self.genotype.bootstrap(strains = _strains, trait = _vals,
- # variance = _vars, nboot=fd.nboot)
- # else:
- # self.bootResult = self.genotype.bootstrap(strains = _strains, trait = _vals,
- # nboot=fd.nboot)
- # else:
- # self.bootResult = []
-
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index c396b14b..605fde63 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -110,6 +110,15 @@ class MarkerRegression(object):
results = self.run_rqtl_geno()
#print("qtl_results:", results)
+ elif self.mapping_method == "reaper":
+ if start_vars['num_perm'] == "":
+ self.num_perm = 0
+ else:
+ self.num_perm = int(start_vars['num_perm'])
+ self.additive = False
+ self.control = start_vars['control_marker']
+ self.do_control = start_vars['do_control']
+ results = self.gen_reaper_results()
elif self.mapping_method == "plink":
results = self.run_plink()
#print("qtl_results:", pf(results))
@@ -130,7 +139,7 @@ class MarkerRegression(object):
if marker['chr1'] > 0 or marker['chr1'] == "X" or marker['chr1'] == "X/Y":
if marker['chr1'] > highest_chr or marker['chr1'] == "X" or marker['chr1'] == "X/Y":
highest_chr = marker['chr1']
- if 'lod_score' in marker:
+ if 'lod_score' in marker.keys():
self.qtl_results.append(marker)
for qtl in enumerate(self.qtl_results):
@@ -157,7 +166,7 @@ class MarkerRegression(object):
if marker['chr'] > 0 or marker['chr'] == "X" or marker['chr'] == "X/Y":
if marker['chr'] > highest_chr or marker['chr'] == "X" or marker['chr'] == "X/Y":
highest_chr = marker['chr']
- if 'lod_score' in marker:
+ if ('lod_score' in marker.keys()) or ('lrs_value' in marker.keys()):
self.qtl_results.append(marker)
self.json_data['chr'] = []
@@ -178,7 +187,7 @@ class MarkerRegression(object):
else:
self.json_data['chr'].append(str(qtl['chr']))
self.json_data['pos'].append(qtl['Mb'])
- if 'lrs_value' in qtl:
+ if 'lrs_value' in qtl.keys():
self.json_data['lod.hk'].append(str(qtl['lrs_value']))
else:
self.json_data['lod.hk'].append(str(qtl['lod_score']))
@@ -588,6 +597,66 @@ class MarkerRegression(object):
return sample_list
+ def gen_reaper_results(self):
+ genotype = self.dataset.group.read_genotype_file()
+
+ samples, values, variances = self.this_trait.export_informative()
+
+ trimmed_samples = []
+ trimmed_values = []
+ for i in range(0, len(samples)):
+ if samples[i] in self.dataset.group.samplelist:
+ trimmed_samples.append(samples[i])
+ trimmed_values.append(values[i])
+
+ self.lrs_array = genotype.permutation(strains = trimmed_samples,
+ trait = trimmed_values,
+ nperm= self.num_perm)
+
+ self.suggestive = self.lrs_array[int(self.num_perm*0.37-1)]
+ self.significant = self.lrs_array[int(self.num_perm*0.95-1)]
+ self.json_data['suggestive'] = self.suggestive
+ self.json_data['significant'] = self.significant
+
+ print("samples:", trimmed_samples)
+
+ if self.control != "" and self.do_control == "true":
+ reaper_results = genotype.regression(strains = trimmed_samples,
+ trait = trimmed_values,
+ control = self.control)
+ else:
+ reaper_results = genotype.regression(strains = trimmed_samples,
+ trait = trimmed_values)
+
+ self.json_data['chr'] = []
+ self.json_data['pos'] = []
+ self.json_data['lod.hk'] = []
+ self.json_data['markernames'] = []
+ if self.additive:
+ self.json_data['additive'] = []
+
+ #Need to convert the QTL objects that qtl reaper returns into a json serializable dictionary
+ qtl_results = []
+ for qtl in reaper_results:
+ reaper_locus = qtl.locus
+ #ZS: Convert chr to int
+ converted_chr = reaper_locus.chr
+ if reaper_locus.chr != "X" and reaper_locus.chr != "X/Y":
+ converted_chr = int(reaper_locus.chr)
+ self.json_data['chr'].append(converted_chr)
+ self.json_data['pos'].append(reaper_locus.Mb)
+ self.json_data['lod.hk'].append(qtl.lrs)
+ self.json_data['markernames'].append(reaper_locus.name)
+ if self.additive:
+ self.json_data['additive'].append(qtl.additive)
+ locus = {"name":reaper_locus.name, "chr":reaper_locus.chr, "cM":reaper_locus.cM, "Mb":reaper_locus.Mb}
+ qtl = {"lrs_value": qtl.lrs, "chr":converted_chr, "Mb":reaper_locus.Mb,
+ "cM":reaper_locus.cM, "name":reaper_locus.name, "additive":qtl.additive, "dominance":qtl.dominance}
+ qtl_results.append(qtl)
+
+ return qtl_results
+
+
def parse_plink_output(self, output_filename):
plink_results={}
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 23d5a631..a7b5fad3 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -178,9 +178,13 @@ class MarkerRegression(object):
self.this_trait = start_vars['this_trait']
self.species = start_vars['species']
- self.vals = start_vars['vals'] #Needed to put into form for when it is resubmitted for single chr views or remapping
-
- self.mapping_method = start_vars['mapping_method'] #Needing for form submission when doing single chr mapping or remapping after changing options
+ #Needing for form submission when doing single chr mapping or remapping after changing options
+ self.vals = start_vars['vals']
+ self.mapping_method = start_vars['mapping_method']
+ if self.mapping_method == "rqtl_geno":
+ self.mapmethod_rqtl_geno = start_vars['method']
+ self.mapmodel_rqtl_geno = start_vars['model']
+ self.pair_scan = start_vars['pair_scan']
self.js_data = start_vars['js_data']
@@ -225,10 +229,15 @@ class MarkerRegression(object):
#self.permChecked = fd.formdata.getvalue('permCheck', True)
self.bootChecked = False #ZS: For now setting to False, I'll add this option later once rest of figure works
#self.bootChecked = fd.formdata.getvalue('bootCheck', '')
+ if 'do_control' in start_vars.keys():
+ self.doControl = start_vars['do_control']
+ else:
+ self.doControl = "false"
if 'control' in start_vars.keys():
self.controlLocus = start_vars['control']
else:
self.controlLocus = ""
+
#self.controlLocus = fd.formdata.getvalue('controlLocus', '')
#try:
@@ -1760,6 +1769,7 @@ class MarkerRegression(object):
lineColor = pid.lightblue
startPosX = xLeftOffset
for j, ChrInfo in enumerate(ChrAInfo):
+ if ChrInfo == self.selectedChr:
preLpos = -1
for i, item in enumerate(ChrInfo):
Lname,Lpos = item
@@ -1932,8 +1942,6 @@ class MarkerRegression(object):
previous_chr = qtlresult['chr']
previous_chr_as_int += 1
- print("ChrLengthDistList:", self.ChrLengthDistList)
-
newStartPosX = (self.ChrLengthDistList[previous_chr_as_int - 1]+self.GraphInterval)*plotXScale
if newStartPosX != oldStartPosX:
startPosX += newStartPosX
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 16eeb8df..a48ac2b7 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -236,9 +236,11 @@
var form_data, url;
console.log("In interval mapping");
//$("#progress_bar_container").modal();
- url = "/interval_mapping";
+ url = "/marker_regression";
$('input[name=method]').val("reaper");
$('input[name=manhattan_plot]').val($('input[name=manhattan_plot_reaper]:checked').val());
+ $('input[name=control_marker]').val($('input[name=control_reaper]').val());
+ $('input[name=do_control]').val($('input[name=do_control_reaper]:checked').val());
$('input[name=mapping_display_all]').val($('input[name=display_all_reaper]'));
$('input[name=suggestive]').val($('input[name=suggestive_reaper]'));
form_data = $('#trait_data_form').serialize();
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index 05623462..9f7dd41f 100644
--- a/wqflask/wqflask/templates/marker_regression_gn1.html
+++ b/wqflask/wqflask/templates/marker_regression_gn1.html
@@ -22,6 +22,11 @@
<input type="hidden" name="selected_chr" value="{{ selectedChr }}">
<input type="hidden" name="manhattan_plot">
<input type="hidden" name="num_perm">
+ <input type="hidden" name="do_control" value="{{ doControl }}">
+ <input type="hidden" name="control_marker" value="{{ controlLocus }}">
+ <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 }}">
<div id="chart_container">
<div class="qtlcharts" id="topchart">
{{ gifmap|safe }}
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index de25f4ee..5b0c74c3 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -187,6 +187,24 @@
<input name="num_perm_reaper" value="2000" type="text" class="form-control">
</div>
</div>
+ <div class="mapping_method_fields form-group">
+ <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_reaper" value="{{ nearest_marker }}" type="text" style="width: 160px;" class="form-control" />
+ {% else %}
+ <input name="control_reaper" value="" type="text" class="form-control" />
+ {% endif %}
+ <label class="radio-inline">
+ <input type="radio" name="do_control_reaper" value="true">
+ Yes
+ </label>
+ <label class="radio-inline">
+ <input type="radio" name="do_control_reaper" value="false" checked="">
+ No
+ </label>
+ </div>
+ </div>
<!--
<div class="mapping_method_fields form-group">
<label for="mapping_bootstraps" class="col-xs-3 control-label" title="Bootstrapping Resamples">Bootstrap</label>
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 9c5a3c92..73d9ddab 100755
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -411,28 +411,6 @@ def marker_regression_page():
return rendered_template
-@app.route("/export", methods = ('POST',))
-def export():
- print("request.form:", request.form)
- svg_xml = request.form.get("data", "Invalid data")
- filename = request.form.get("filename", "manhattan_plot_snp")
- response = Response(svg_xml, mimetype="image/svg+xml")
- response.headers["Content-Disposition"] = "attachment; filename=%s"%filename
- return response
-
-@app.route("/export_pdf", methods = ('POST',))
-def export_pdf():
- import cairosvg
- print("request.form:", request.form)
- svg_xml = request.form.get("data", "Invalid data")
- print("svg_xml:", svg_xml)
- filename = request.form.get("filename", "interval_map_pdf")
- filepath = "/home/zas1024/gene/wqflask/output/"+filename
- pdf_file = cairosvg.svg2pdf(bytestring=svg_xml)
- response = Response(pdf_file, mimetype="application/pdf")
- response.headers["Content-Disposition"] = "attachment; filename=%s"%filename
- return response
-
@app.route("/interval_mapping", methods=('POST',))
def interval_mapping_page():
initial_start_vars = request.form
@@ -487,6 +465,28 @@ def interval_mapping_page():
return rendered_template
+@app.route("/export", methods = ('POST',))
+def export():
+ print("request.form:", request.form)
+ svg_xml = request.form.get("data", "Invalid data")
+ filename = request.form.get("filename", "manhattan_plot_snp")
+ response = Response(svg_xml, mimetype="image/svg+xml")
+ response.headers["Content-Disposition"] = "attachment; filename=%s"%filename
+ return response
+
+@app.route("/export_pdf", methods = ('POST',))
+def export_pdf():
+ import cairosvg
+ print("request.form:", request.form)
+ svg_xml = request.form.get("data", "Invalid data")
+ print("svg_xml:", svg_xml)
+ filename = request.form.get("filename", "interval_map_pdf")
+ filepath = "/home/zas1024/gene/wqflask/output/"+filename
+ pdf_file = cairosvg.svg2pdf(bytestring=svg_xml)
+ response = Response(pdf_file, mimetype="application/pdf")
+ response.headers["Content-Disposition"] = "attachment; filename=%s"%filename
+ return response
+
@app.route("/corr_compute", methods=('POST',))
def corr_compute_page():
print("In corr_compute, request.form is:", pf(request.form))