Merge branch 'build/python3-migration' of github.com:BonfaceKilz/genenetwork2 into build/python3-migration

1 files changed, 27 insertions, 29 deletions

diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py
index b9b71129..61f408d2 100644
--- a/wqflask/utility/Plot.py
+++ b/wqflask/utility/Plot.py
@@ -24,15 +24,13 @@
 #
 # Last updated by GeneNetwork Core Team 2010/10/20
 
-from __future__ import print_function
-
 from PIL import ImageColor
 from PIL import ImageDraw
 from PIL import ImageFont
 
 from math import *
 
-import corestats
+import utility.corestats as corestats
 from base import webqtlConfig
 from utility.pillow_utils import draw_rotated_text
 import utility.logger
@@ -54,7 +52,7 @@ def cformat(d, rank=0):
     strD = "%2.6f" % d
 
     if rank == 0:
-        while strD[-1] in ('0','.'):
+        while strD[-1] in ('0', '.'):
             if strD[-1] == '0' and strD[-2] == '.' and len(strD) <= 4:
                 break
             elif strD[-1] == '.':
@@ -82,7 +80,7 @@ def frange(start, end=None, inc=1.0):
     # Need to adjust the count. AFAICT, it always comes up one short.
         count += 1
     L = [start] * count
-    for i in xrange(1, count):
+    for i in range(1, count):
         L[i] = start + i * inc
     return L
 
@@ -93,7 +91,7 @@ def find_outliers(vals):
     >>> find_outliers([3.504, 5.234, 6.123, 7.234, 3.542, 5.341, 7.852, 4.555, 12.537])
     (11.252500000000001, 0.5364999999999993)
 
-    >>> >>> find_outliers([9,12,15,17,31,50,7,5,6,8])
+    >>> find_outliers([9,12,15,17,31,50,7,5,6,8])
     (32.0, -8.0)
 
     If there are no vals, returns None for the upper and lower bounds,
@@ -158,7 +156,7 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab
        j = int((item-xLow)/step)
        Count[j] += 1
 
-    yLow, yTop, stepY=detScale(0,max(Count))
+    yLow, yTop, stepY=detScale(0, max(Count))
 
     #draw data
     xScale = plotWidth/(xTop-xLow)
@@ -170,7 +168,7 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab
            xc = (dataXY[i]-xLow)*xScale+xLeftOffset
            yc =-(count-yLow)*yScale+yTopOffset+plotHeight
            im_drawer.rectangle(
-               xy=((xc+2,yc),(xc+barWidth-2,yTopOffset+plotHeight)),
+               xy=((xc+2, yc), (xc+barWidth-2, yTopOffset+plotHeight)),
                outline=barColor, fill=barColor)
 
     #draw drawing region
@@ -179,81 +177,81 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab
     )
 
     #draw scale
-    scaleFont=ImageFont.truetype(font=COUR_FILE,size=11)
+    scaleFont=ImageFont.truetype(font=COUR_FILE, size=11)
     x=xLow
     for i in range(int(stepX)+1):
        xc=xLeftOffset+(x-xLow)*xScale
        im_drawer.line(
-           xy=((xc,yTopOffset+plotHeight),(xc,yTopOffset+plotHeight+5)),
+           xy=((xc, yTopOffset+plotHeight), (xc, yTopOffset+plotHeight+5)),
            fill=axesColor)
        strX = cformat(d=x, rank=0)
        im_drawer.text(
            text=strX,
-           xy=(xc-im_drawer.textsize(strX,font=scaleFont)[0]/2,
-               yTopOffset+plotHeight+14),font=scaleFont)
+           xy=(xc-im_drawer.textsize(strX, font=scaleFont)[0]/2,
+               yTopOffset+plotHeight+14), font=scaleFont)
        x+= (xTop - xLow)/stepX
 
     y=yLow
     for i in range(int(stepY)+1):
        yc=yTopOffset+plotHeight-(y-yLow)*yScale
-       im_drawer.line(xy=((xLeftOffset,yc),(xLeftOffset-5,yc)), fill=axesColor)
+       im_drawer.line(xy=((xLeftOffset, yc), (xLeftOffset-5, yc)), fill=axesColor)
        strY = "%d" %y
        im_drawer.text(
            text=strY,
-           xy=(xLeftOffset-im_drawer.textsize(strY,font=scaleFont)[0]-6,yc+5),
+           xy=(xLeftOffset-im_drawer.textsize(strY, font=scaleFont)[0]-6, yc+5),
            font=scaleFont)
        y+= (yTop - yLow)/stepY
 
     #draw label
-    labelFont=ImageFont.truetype(font=TAHOMA_FILE,size=17)
+    labelFont=ImageFont.truetype(font=TAHOMA_FILE, size=17)
     if XLabel:
        im_drawer.text(
            text=XLabel,
            xy=(xLeftOffset+(
-               plotWidth-im_drawer.textsize(XLabel,font=labelFont)[0])/2.0,
+               plotWidth-im_drawer.textsize(XLabel, font=labelFont)[0])/2.0,
                yTopOffset+plotHeight+yBottomOffset-10),
-           font=labelFont,fill=labelColor)
+           font=labelFont, fill=labelColor)
 
     if YLabel:
         draw_rotated_text(canvas, text=YLabel,
                           xy=(19,
                               yTopOffset+plotHeight-(
                                   plotHeight-im_drawer.textsize(
-                                      YLabel,font=labelFont)[0])/2.0),
+                                      YLabel, font=labelFont)[0])/2.0),
                           font=labelFont, fill=labelColor, angle=90)
 
-    labelFont=ImageFont.truetype(font=VERDANA_FILE,size=16)
+    labelFont=ImageFont.truetype(font=VERDANA_FILE, size=16)
     if title:
        im_drawer.text(
            text=title,
            xy=(xLeftOffset+(plotWidth-im_drawer.textsize(
-               title,font=labelFont)[0])/2.0,
+               title, font=labelFont)[0])/2.0,
                20),
-           font=labelFont,fill=labelColor)
+           font=labelFont, fill=labelColor)
 
 # This function determines the scale of the plot
-def detScaleOld(min,max):
+def detScaleOld(min, max):
     if min>=max:
         return None
     elif min == -1.0 and max == 1.0:
-        return [-1.2,1.2,12]
+        return [-1.2, 1.2, 12]
     else:
         a=max-min
         b=floor(log10(a))
-        c=pow(10.0,b)
+        c=pow(10.0, b)
         if a < c*5.0:
             c/=2.0
         #print a,b,c
         low=c*floor(min/c)
         high=c*ceil(max/c)
-        return [low,high,round((high-low)/c)]
+        return [low, high, round((high-low)/c)]
 
 def detScale(min=0,max=0):
 
     if min>=max:
         return None
     elif min == -1.0 and max == 1.0:
-        return [-1.2,1.2,12]
+        return [-1.2, 1.2, 12]
     else:
         a=max-min
         if max != 0:
@@ -265,7 +263,7 @@ def detScale(min=0,max=0):
                 min -= 0.1*a
         a=max-min
         b=floor(log10(a))
-        c=pow(10.0,b)
+        c=pow(10.0, b)
         low=c*floor(min/c)
         high=c*ceil(max/c)
         n = round((high-low)/c)
@@ -283,7 +281,7 @@ def detScale(min=0,max=0):
             high=c*ceil(max/c)
             n = round((high-low)/c)
 
-        return [low,high,n]
+        return [low, high, n]
 
 def bluefunc(x):
     return 1.0 / (1.0 + exp(-10*(x-0.6)))
@@ -292,7 +290,7 @@ def redfunc(x):
     return 1.0 / (1.0 + exp(10*(x-0.5)))
 
 def greenfunc(x):
-    return 1 - pow(redfunc(x+0.2),2) - bluefunc(x-0.3)
+    return 1 - pow(redfunc(x+0.2), 2) - bluefunc(x-0.3)
 
 def colorSpectrum(n=100):
     multiple = 10