diff options
| -rwxr-xr-x | wqflask/htmlgen.py | 14 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/marker_regression_gn1.py | 47 | ||||
| -rwxr-xr-x | wqflask/wqflask/views.py | 17 |
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it""" - def __getattr__(self, name): - return "" - - def Item(self, *args, **kw): - print("This way of generating html is obsolete!")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) |