aboutsummaryrefslogtreecommitdiff
path: root/wqflask
diff options
context:
space:
mode:
authorzsloan2015-05-08 21:25:55 +0000
committerzsloan2015-05-08 21:25:55 +0000
commit8bffd6487c4848ed9471487b3dbbdd56b1884e0c (patch)
tree99e6529990178381ae7a05ceb4474a4935c3f255 /wqflask
parenta3342afd77425eb8edaaef0b09ee1b88c79dfdfc (diff)
downloadgenenetwork2-8bffd6487c4848ed9471487b3dbbdd56b1884e0c.tar.gz
Committing before pulling latest changes/fixes
Diffstat (limited to 'wqflask')
-rwxr-xr-xwqflask/wqflask/marker_regression/marker_regression.py128
-rw-r--r--wqflask/wqflask/templates/pair_scan_results.html2
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 @@
</tr>
</thead>
<tbody>
- {% for marker in pair_scan_results %}
+ {% for marker in filtered_markers %}
<tr>
<td>{{loop.index}}</td>
<td>{{marker.name}}</td>