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-rwxr-xr-xwqflask/htmlgen.py14
-rw-r--r--wqflask/wqflask/marker_regression/marker_regression_gn1.py47
-rwxr-xr-xwqflask/wqflask/views.py17
3 files changed, 39 insertions, 39 deletions
diff --git a/wqflask/htmlgen.py b/wqflask/htmlgen.py
deleted file mode 100755
index 8406d925..00000000
--- a/wqflask/htmlgen.py
+++ /dev/null
@@ -1,14 +0,0 @@
-from __future__ import absolute_import, division, print_function
-
-class HTMLgen(object):
- """A redefined HT until we manage to completely eliminate it"""
- def __getattr__(self, name):
- return ""
-
- def Item(self, *args, **kw):
- print("This way of generating html is obsolete!")
- return "foo"
-
- Href = Span = TD = Blockquote = Image = Item
-
-HTMLgen2 = HTMLgen()
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 5deeb305..c838b3ec 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -626,6 +626,9 @@ class MarkerRegression(object):
self.dict['body'] = TD_LR
self.dict['title'] = "Mapping"
+
+ print("AT END OF GN1 MAPPING")
+
def writeQTL2Text(self, filename):
if self.multipleInterval:
return ""
@@ -756,7 +759,8 @@ class MarkerRegression(object):
drawAreaHeight -= 60
#Image map
- gifmap = HT.Map(name='WebQTLImageMap')
+ gifmap = HT.Map(name = "WebQTLImageMap")
+ #gifmap = None
newoffset = (xLeftOffset, xRightOffset, yTopOffset, yBottomOffset)
# Draw the alternating-color background first and get plotXScale
@@ -1689,7 +1693,7 @@ class MarkerRegression(object):
distScale = 10
else:
distScale = 5
- for tickdists in range(distScale, ceil(distLen), distScale):
+ for tickdists in range(distScale, int(ceil(distLen)), distScale):
canvas.drawLine(startPosX + tickdists*plotXScale, yZero, startPosX + tickdists*plotXScale, yZero + 7, color=pid.black, width=1*zoom)
canvas.drawString(str(tickdists), startPosX+tickdists*plotXScale, yZero + 10*zoom, color=pid.black, font=MBLabelFont, angle=270)
startPosX += (self.ChrLengthDistList[i]+self.GraphInterval)*plotXScale
@@ -1809,7 +1813,12 @@ class MarkerRegression(object):
lodm = 1.0
if self.lrsMax <= 0: #sliding scale
- LRSMax = max(map(max, self.qtlresults)).lrs
+ if "lrs_value" in self.qtlresults[0]:
+ LRSMax = max([result['lrs_value'] for result in self.qtlresults])
+ #LRSMax = max(map(max, self.qtlresults)).lrs_value
+ else:
+ LRSMax = max([result['lod_score'] for result in self.qtlresults])
+ #LRSMax = max(map(max, self.qtlresults)).lod_score
#genotype trait will give infinite LRS
LRSMax = min(LRSMax, webqtlConfig.MAXLRS)
if self.permChecked and not self.multipleInterval:
@@ -1882,11 +1891,11 @@ class MarkerRegression(object):
if self.multipleInterval:
lrsEdgeWidth = 1
else:
- additiveMax = max(map(lambda X : abs(X.additive), self.qtlresults[0]))
- if INTERCROSS:
- dominanceMax = max(map(lambda X : abs(X.dominance), self.qtlresults[0]))
- else:
- dominanceMax = -1
+ #additiveMax = max(map(lambda X : abs(X.additive), self.qtlresults[0]))
+ #if INTERCROSS:
+ # dominanceMax = max(map(lambda X : abs(X.dominance), self.qtlresults[0]))
+ #else:
+ # dominanceMax = -1
lrsEdgeWidth = 2
if zoom == 2:
@@ -1894,7 +1903,7 @@ class MarkerRegression(object):
for i, qtlresult in enumerate(self.qtlresults):
m = 0
startPosX = xLeftOffset
- thisLRSColor = self.colorCollection[i]
+ thisLRSColor = self.colorCollection[0]
for j, _chr in enumerate(self.genotype):
LRSCoordXY = []
AdditiveCoordXY = []
@@ -1907,20 +1916,20 @@ class MarkerRegression(object):
# updated by NL 06-18-2011:
# fix the over limit LRS graph issue since genotype trait may give infinite LRS;
# for any lrs is over than 460(LRS max in this system), it will be reset to 460
- if qtlresult[m].lrs> 460 or qtlresult[m].lrs=='inf':
+ if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value']=='inf':
Yc = yZero - webqtlConfig.MAXLRS*LRSHeightThresh/LRSMax
else:
- Yc = yZero - qtlresult[m].lrs*LRSHeightThresh/LRSMax
+ Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/LRSMax
LRSCoordXY.append((Xc, Yc))
- if not self.multipleInterval and self.additiveChecked:
- if additiveMax == 0.0:
- additiveMax = 0.000001
- Yc = yZero - qtlresult[m].additive*AdditiveHeightThresh/additiveMax
- AdditiveCoordXY.append((Xc, Yc))
- if not self.multipleInterval and INTERCROSS and self.additiveChecked:
- Yc = yZero - qtlresult[m].dominance*DominanceHeightThresh/dominanceMax
- DominanceCoordXY.append((Xc, Yc))
+ #if not self.multipleInterval and self.additiveChecked:
+ # if additiveMax == 0.0:
+ # additiveMax = 0.000001
+ # Yc = yZero - qtlresult[m].additive*AdditiveHeightThresh/additiveMax
+ # AdditiveCoordXY.append((Xc, Yc))
+ #if not self.multipleInterval and INTERCROSS and self.additiveChecked:
+ # Yc = yZero - qtlresult[m].dominance*DominanceHeightThresh/dominanceMax
+ # DominanceCoordXY.append((Xc, Yc))
m += 1
canvas.drawPolygon(LRSCoordXY,edgeColor=thisLRSColor,closed=0, edgeWidth=lrsEdgeWidth, clipX=(xLeftOffset, xLeftOffset + plotWidth))
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 3b100fa6..23c74817 100755
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -354,11 +354,12 @@ def marker_regression_page():
if key in wanted or key.startswith(('value:')):
start_vars[key] = value
- version = "v1"
+ version = "v3"
key = "marker_regression:{}:".format(version) + json.dumps(start_vars, sort_keys=True)
print("key is:", pf(key))
with Bench("Loading cache"):
- result = Redis.get(key)
+ result = None # Just for testing
+ #result = Redis.get(key)
#print("************************ Starting result *****************")
#print("result is [{}]: {}".format(type(result), result))
@@ -377,14 +378,18 @@ def marker_regression_page():
indent=" ")
result = template_vars.__dict__
- print("initial result:", result['qtl_results'])
+ #print("initial result:", result['qtl_results'])
- for item in template_vars.__dict__.keys():
- print(" ---**--- {}: {}".format(type(template_vars.__dict__[item]), item))
+ #for item in template_vars.__dict__.keys():
+ # print(" ---**--- {}: {}".format(type(template_vars.__dict__[item]), item))
#causeerror
- gn1_template_vars = marker_regression_gn1.MarkerRegression(result)
+ print("TESTING GN1!!!")
+ gn1_template_vars = marker_regression_gn1.MarkerRegression(result).__dict__
+ print("gn1_template_vars:", gn1_template_vars)
+ causeerror
+
#qtl_length = len(result['js_data']['qtl_results'])
#print("qtl_length:", qtl_length)
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 22:01:03 +0000