From 8bffd6487c4848ed9471487b3dbbdd56b1884e0c Mon Sep 17 00:00:00 2001 From: zsloan Date: Fri, 8 May 2015 21:25:55 +0000 Subject: Committing before pulling latest changes/fixes --- .../wqflask/marker_regression/marker_regression.py | 128 +++++++++++++-------- wqflask/wqflask/templates/pair_scan_results.html | 2 +- 2 files changed, 78 insertions(+), 52 deletions(-) diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index 49521bd6..b3f6d0bb 100755 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -120,57 +120,83 @@ class MarkerRegression(object): else: print("RUNNING NOTHING") - self.lod_cutoff = 2 - self.filtered_markers = [] - highest_chr = 1 #This is needed in order to convert the highest chr to X/Y - for marker in qtl_results: - 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: - self.filtered_markers.append(marker) - - self.json_data['chr'] = [] - self.json_data['pos'] = [] - self.json_data['lod.hk'] = [] - self.json_data['markernames'] = [] - - self.json_data['suggestive'] = self.suggestive - self.json_data['significant'] = self.significant - - #Need to convert the QTL objects that qtl reaper returns into a json serializable dictionary - self.qtl_results = [] - for index,qtl in enumerate(self.filtered_markers): - 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") - self.json_data['chr'].append("X") - else: - self.json_data['chr'].append(str(qtl['chr'])) - self.json_data['pos'].append(qtl['Mb']) - self.json_data['lod.hk'].append(str(qtl['lod_score'])) - self.json_data['markernames'].append(qtl['name']) - - #Get chromosome lengths for drawing the interval map plot - chromosome_mb_lengths = {} - self.json_data['chrnames'] = [] - for key in self.species.chromosomes.chromosomes.keys(): - self.json_data['chrnames'].append([self.species.chromosomes.chromosomes[key].name, self.species.chromosomes.chromosomes[key].mb_length]) - chromosome_mb_lengths[key] = self.species.chromosomes.chromosomes[key].mb_length - - # print("json_data:", self.json_data) - - - self.js_data = dict( - json_data = self.json_data, - this_trait = self.this_trait.name, - data_set = self.dataset.name, - maf = self.maf, - manhattan_plot = self.manhattan_plot, - chromosomes = chromosome_mb_lengths, - qtl_results = self.filtered_markers, - ) + if self.pair_scan == True: + self.filtered_markers = [] + highest_chr = 1 #This is needed in order to convert the highest chr to X/Y + for marker in qtl_results: + 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: + self.filtered_markers.append(marker) + + for qtl in enumerate(self.filtered_markers): + self.json_data['chr1'].append(str(qtl['chr1'])) + self.json_data['chr2'].append(str(qtl['chr2'])) + self.json_data['Mb'].append(qtl['Mb']) + self.json_data['markernames'].append(qtl['name']) + + self.js_data = dict( + json_data = self.json_data, + this_trait = self.this_trait.name, + data_set = self.dataset.name, + maf = self.maf, + manhattan_plot = self.manhattan_plot, + qtl_results = self.filtered_markers, + ) + + else: + self.lod_cutoff = 2 + self.filtered_markers = [] + highest_chr = 1 #This is needed in order to convert the highest chr to X/Y + for marker in qtl_results: + 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: + self.filtered_markers.append(marker) + + self.json_data['chr'] = [] + self.json_data['pos'] = [] + self.json_data['lod.hk'] = [] + self.json_data['markernames'] = [] + + self.json_data['suggestive'] = self.suggestive + self.json_data['significant'] = self.significant + + #Need to convert the QTL objects that qtl reaper returns into a json serializable dictionary + self.qtl_results = [] + for index, qtl in enumerate(self.filtered_markers): + 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") + self.json_data['chr'].append("X") + else: + self.json_data['chr'].append(str(qtl['chr'])) + self.json_data['pos'].append(qtl['Mb']) + self.json_data['lod.hk'].append(str(qtl['lod_score'])) + self.json_data['markernames'].append(qtl['name']) + + #Get chromosome lengths for drawing the interval map plot + chromosome_mb_lengths = {} + self.json_data['chrnames'] = [] + for key in self.species.chromosomes.chromosomes.keys(): + self.json_data['chrnames'].append([self.species.chromosomes.chromosomes[key].name, self.species.chromosomes.chromosomes[key].mb_length]) + chromosome_mb_lengths[key] = self.species.chromosomes.chromosomes[key].mb_length + + # print("json_data:", self.json_data) + + + self.js_data = dict( + json_data = self.json_data, + this_trait = self.this_trait.name, + data_set = self.dataset.name, + maf = self.maf, + manhattan_plot = self.manhattan_plot, + chromosomes = chromosome_mb_lengths, + qtl_results = self.filtered_markers, + ) def run_gemma(self): diff --git a/wqflask/wqflask/templates/pair_scan_results.html b/wqflask/wqflask/templates/pair_scan_results.html index f46d7cbf..ab4a36bb 100644 --- a/wqflask/wqflask/templates/pair_scan_results.html +++ b/wqflask/wqflask/templates/pair_scan_results.html @@ -44,7 +44,7 @@ - {% for marker in pair_scan_results %} + {% for marker in filtered_markers %} {{loop.index}} {{marker.name}} -- cgit v1.2.3