diff options
| -rwxr-xr-x | wqflask/wqflask/marker_regression/marker_regression.py | 61 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/marker_regression_gn1.html | 20 | ||||
| -rwxr-xr-x | wqflask/wqflask/views.py | 14 |
3 files changed, 69 insertions, 26 deletions
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index 37f9351d..b75a30f6 100755 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -18,6 +18,7 @@ import numpy as np from scipy import linalg import cPickle as pickle +import itertools import simplejson as json @@ -90,10 +91,14 @@ class MarkerRegression(object): self.dataset.group.get_markers() if self.mapping_method == "gemma": self.score_type = "LOD" - included_markers, p_values = gemma_mapping.run_gemma(self.dataset, self.samples, self.vals) - self.dataset.group.get_specified_markers(markers = included_markers) - self.dataset.group.markers.add_pvalues(p_values) - results = self.dataset.group.markers.markers + with Bench("Running GEMMA"): + included_markers, p_values = gemma_mapping.run_gemma(self.dataset, self.samples, self.vals) + with Bench("Getting markers from csv"): + marker_obs = get_markers_from_csv(included_markers, p_values, self.dataset.group.name) + results = marker_obs + #self.dataset.group.get_specified_markers(markers = included_markers) + #self.dataset.group.markers.add_pvalues(p_values) + #results = self.dataset.group.markers.markers elif self.mapping_method == "rqtl_plink": results = self.run_rqtl_plink() elif self.mapping_method == "rqtl_geno": @@ -183,7 +188,7 @@ class MarkerRegression(object): #if index<40: # print("lod score is:", qtl['lod_score']) if qtl['chr'] == highest_chr and highest_chr != "X" and highest_chr != "X/Y": - print("changing to X") + #print("changing to X") self.json_data['chr'].append("X") else: self.json_data['chr'].append(str(qtl['chr'])) @@ -1006,6 +1011,52 @@ def create_snp_iterator_file(group): with gzip.open(snp_file_base, "wb") as fh: pickle.dump(data, fh, pickle.HIGHEST_PROTOCOL) +def get_markers_from_csv(included_markers, p_values, group_name): + marker_data_fh = open(os.path.join(webqtlConfig.PYLMM_PATH + group_name + '_markers.csv')) + markers = [] + for marker_name, p_value in itertools.izip(included_markers, p_values): + if not p_value or len(included_markers) < 1: + continue + for line in marker_data_fh: + splat = line.strip().split() + if splat[0] == marker_name: + marker = {} + marker['name'] = splat[0] + marker['chr'] = int(splat[1]) + marker['Mb'] = float(splat[2]) + marker['p_value'] = p_value + 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 + markers.append(marker) + break + +# for line, p_value in itertools.izip(marker_data_fh, p_values): +# if not p_value or len(included_markers) < 1: +# continue +# splat = line.strip().split() +# if splat[0] in included_markers: +# marker = {} +# marker['name'] = splat[0] +# marker['chr'] = int(splat[1]) +# marker['Mb'] = float(splat[2]) +# marker['p_value'] = p_value +# 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 +# markers.append(marker) +# else: +# continue + + return markers + + #if __name__ == '__main__': # import cPickle as pickle # import gzip diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html index 4eb5862a..58478758 100644 --- a/wqflask/wqflask/templates/marker_regression_gn1.html +++ b/wqflask/wqflask/templates/marker_regression_gn1.html @@ -15,7 +15,6 @@ <input type="hidden" name="trait_id" value="{{ this_trait.name }}"> <input type="hidden" name="dataset" value="{{ dataset.name }}"> <input type="hidden" name="method" value="{{ mapping_method }}"> - {% if mapping_method != "gemma" %} {% for sample in dataset.group.samplelist %} <input type="hidden" name="value:{{ sample }}" value="{{ vals[loop.index - 1] }}"> {% endfor %} @@ -29,7 +28,6 @@ <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 }}"> - {% endif %} <div class="container"> <div class="col-xs-5"> @@ -42,7 +40,6 @@ <b>Location:</b> Chr {{ this_trait.chr }} @ {{ this_trait.mb }} Mb {% endif %} </div> - {% if mapping_method != "gemma" %} <div id="gn1_map_options" class="col-xs-5" style="border:2px solid black; padding: 10px; margin: 10px;"> <div class="col-xs-7" style="padding-left: 0px;"> <table> @@ -69,40 +66,37 @@ </div> </div> </div> - {% endif %} - <div class="tabbable" style="margin: 10px;"> <ul class="nav nav-tabs"> - {% if mapping_method != "gemma" %} <li id="gn1_map_tab"> <a href="#gn1_map" data-toggle="tab" aria-expanded="true">GN1 Map</a> </li> - {% endif %} + {% if mapping_method != "gemma" %} <li id="vector_map_tab"> <a href="#vector_map" data-toggle="tab" {% if mapping_method != "gemma" %}aria-expanded="false"{% else %}aria-expanded="true"{% endif %}>Vector Map</a> </li> + {% endif %} </ul> <div class="tab-content"> - {% if mapping_method != "gemma" %} <div class="tab-pane active" id="gn1_map"> <div class="qtlcharts"> {{ gifmap|safe }} <img src="/static/output/{{ filename }}.jpeg" usemap="#WebQTLImageMap"> </div> </div> - {% endif %} + {% if mapping_method != "gemma" %} <div class="tab-pane {% if mapping_method == "gemma" %}active{% endif %}" id="vector_map"> <div id="chart_container"> <div class="qtlcharts" id="topchart"></div> </div> </div> + {% endif %} </div> </div> </form> - - {% if mapping_method != "gemma" %} + {% if mapping_method != "gemma" %} <div style="width:48%;"> <h2> Results @@ -182,11 +176,13 @@ js_data = {{ js_data | safe }} </script> + {% if mapping_method != "gemma" %} <script language="javascript" type="text/javascript" src="/static/new/javascript/panelutil.js"></script> <script language="javascript" type="text/javascript" src="/static/new/javascript/chr_lod_chart.js"></script> <script language="javascript" type="text/javascript" src="/static/new/javascript/lod_chart.js"></script> <script language="javascript" type="text/javascript" src="/static/new/javascript/create_lodchart.js"></script> - + {% endif %} + <script type="text/javascript" charset="utf-8"> $(document).ready( function () { console.time("Creating table"); diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index 17845826..2af03f96 100755 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -380,25 +380,24 @@ def marker_regression_page(): result = pickle.loads(result) else: print("Cache miss!!!") - template_vars = marker_regression.MarkerRegression(start_vars, temp_uuid) + with Bench("Total time in MarkerRegression"): + template_vars = marker_regression.MarkerRegression(start_vars, temp_uuid) template_vars.js_data = json.dumps(template_vars.js_data, default=json_default_handler, indent=" ") result = template_vars.__dict__ - #print("initial result:", result['qtl_results']) #for item in template_vars.__dict__.keys(): # print(" ---**--- {}: {}".format(type(template_vars.__dict__[item]), item)) - if start_vars['method'] != "gemma": - gn1_template_vars = marker_regression_gn1.MarkerRegression(result).__dict__ + gn1_template_vars = marker_regression_gn1.MarkerRegression(result).__dict__ #qtl_length = len(result['js_data']['qtl_results']) #print("qtl_length:", qtl_length) pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL) - print("pickled result length:", len(pickled_result)) + #print("pickled result length:", len(pickled_result)) Redis.set(key, pickled_result) Redis.expire(key, 1*60) @@ -416,10 +415,7 @@ def marker_regression_page(): rendered_template = render_template("pair_scan_results.html", **result) else: #rendered_template = render_template("marker_regression.html", **result) - if start_vars['method'] != "gemma": - rendered_template = render_template("marker_regression_gn1.html", **gn1_template_vars) - else: - rendered_template = render_template("marker_regression_gn1.html", **result) + rendered_template = render_template("marker_regression_gn1.html", **gn1_template_vars) return rendered_template |