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-rw-r--r--wqflask/base/trait.py50
1 files changed, 48 insertions, 2 deletions
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index ce3a7608..51a4d986 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -2,7 +2,7 @@ from __future__ import absolute_import, division, print_function
import string
import resource
-
+import codecs
from htmlgen import HTMLgen2 as HT
@@ -309,6 +309,42 @@ class GeneralTrait(object):
holder = unicode(trait_info[i], "utf8", "ignore")
setattr(self, field, holder)
+ description_string = unicode(str(self.description).strip(codecs.BOM_UTF8), 'utf-8')
+ target_string = unicode(str(self.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8')
+
+ if len(description_string) > 1 and description_string != 'None':
+ description_display = description_string
+ else:
+ description_display = self.symbol
+
+ if (len(description_display) > 1 and description_display != 'N/A' and
+ len(target_string) > 1 and target_string != 'None'):
+ description_display = description_display + '; ' + target_string.strip()
+
+ # Save it for the jinja2 template
+ self.description_display = description_display
+
+ #XZ: trait_location_value is used for sorting
+ trait_location_repr = 'N/A'
+ trait_location_value = 1000000
+
+ if self.chr and self.mb:
+ #Checks if the chromosome number can be cast to an int (i.e. isn't "X" or "Y")
+ #This is so we can convert the location to a number used for sorting
+ trait_location_value = convert_location_to_value(self.chr, self.mb)
+ #try:
+ # trait_location_value = int(self.chr)*1000 + self.mb
+ #except ValueError:
+ # if self.chr.upper() == 'X':
+ # trait_location_value = 20*1000 + self.mb
+ # else:
+ # trait_location_value = (ord(str(self.chr).upper()[0])*1000 +
+ # self.mb)
+
+ #ZS: Put this in function currently called "convert_location_to_value"
+ self.location_repr = 'Chr%s: %.6f' % (self.chr, float(self.mb))
+ self.location_value = trait_location_value
+
if self.dataset.type == 'Publish':
self.confidential = 0
if self.pre_publication_description and not self.pubmed_id:
@@ -662,7 +698,17 @@ class GeneralTrait(object):
ZValue = ZValue*sqrt(self.overlap-3)
self.p_value = 2.0*(1.0 - reaper.normp(abs(ZValue)))
-
+def convert_location_to_value(chromosome, mb):
+ try:
+ location_value = int(chromosome)*1000 + float(mb)
+ except ValueError:
+ if chromosome.upper() == 'X':
+ location_value = 20*1000 + float(mb)
+ else:
+ location_value = (ord(str(chromosome).upper()[0])*1000 +
+ float(mb))
+
+ return location_value
@app.route("/trait/get_sample_data")
def get_sample_data():