autopep8: Fix E101, E11

4 files changed, 126 insertions, 126 deletions

diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py
index 00658d10..f61e3b88 100644
--- a/wqflask/utility/Plot.py
+++ b/wqflask/utility/Plot.py
@@ -79,7 +79,7 @@ def frange(start, end=None, inc=1.0):
         start += 0.0  # force it to be a float
     count = int((end - start) / inc)
     if start + count * inc != end:
-    # Need to adjust the count. AFAICT, it always comes up one short.
+        # Need to adjust the count. AFAICT, it always comes up one short.
         count += 1
     L = [start] * count
     for i in range(1, count):
@@ -131,16 +131,16 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab
     plotWidth = canvas.size[0] - xLeftOffset - xRightOffset
     plotHeight = canvas.size[1] - yTopOffset - yBottomOffset
     if plotHeight <= 0 or plotWidth <= 0:
-       return
+        return
 
     if len(data) < 2:
-       return
+        return
 
     max_D = max(data)
     min_D = min(data)
     # add by NL 06-20-2011: fix the error: when max_D is infinite, log function in detScale will go wrong
     if max_D == float('inf') or max_D > webqtlConfig.MAXLRS:
-       max_D = webqtlConfig.MAXLRS  # maximum LRS value
+        max_D = webqtlConfig.MAXLRS  # maximum LRS value
 
     xLow, xTop, stepX = detScale(min_D, max_D)
 
@@ -151,15 +151,15 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab
     dataXY = []
     Count = []
     while j <= xTop:
-       dataXY.append(j)
-       Count.append(0)
-       j += step
+        dataXY.append(j)
+        Count.append(0)
+        j += step
 
     for i, item in enumerate(data):
-       if item == float('inf') or item > webqtlConfig.MAXLRS:
-           item = webqtlConfig.MAXLRS  # maximum LRS value
-       j = int((item - xLow) / step)
-       Count[j] += 1
+        if item == float('inf') or item > webqtlConfig.MAXLRS:
+            item = webqtlConfig.MAXLRS  # maximum LRS value
+        j = int((item - xLow) / step)
+        Count[j] += 1
 
     yLow, yTop, stepY = detScale(0, max(Count))
 
@@ -169,12 +169,12 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab
     barWidth = xScale * step
 
     for i, count in enumerate(Count):
-       if count:
-           xc = (dataXY[i] - xLow) * xScale + xLeftOffset
-           yc = -(count - yLow) * yScale + yTopOffset + plotHeight
-           im_drawer.rectangle(
-               xy=((xc + 2, yc), (xc + barWidth - 2, yTopOffset + plotHeight)),
-               outline=barColor, fill=barColor)
+        if count:
+            xc = (dataXY[i] - xLow) * xScale + xLeftOffset
+            yc = -(count - yLow) * yScale + yTopOffset + plotHeight
+            im_drawer.rectangle(
+                xy=((xc + 2, yc), (xc + barWidth - 2, yTopOffset + plotHeight)),
+                outline=barColor, fill=barColor)
 
     # draw drawing region
     im_drawer.rectangle(
@@ -186,39 +186,39 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab
     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)),
-           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)
-       x += (xTop - xLow) / stepX
+        xc = xLeftOffset + (x - xLow) * xScale
+        im_drawer.line(
+            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)
+        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)
-       strY = "%d" % y
-       im_drawer.text(
-           text=strY,
-           xy=(xLeftOffset - im_drawer.textsize(strY,
-               font=scaleFont)[0] - 6, yc + 5),
-           font=scaleFont)
-       y += (yTop - yLow) / stepY
+        yc = yTopOffset + plotHeight - (y - yLow) * yScale
+        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),
+            font=scaleFont)
+        y += (yTop - yLow) / stepY
 
     # draw label
     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,
-               yTopOffset + plotHeight + yBottomOffset-10),
-           font=labelFont, fill=labelColor)
+        im_drawer.text(
+            text=XLabel,
+            xy=(xLeftOffset + (
+                plotWidth - im_drawer.textsize(XLabel, font=labelFont)[0]) / 2.0,
+                yTopOffset + plotHeight + yBottomOffset-10),
+            font=labelFont, fill=labelColor)
 
     if YLabel:
         draw_rotated_text(canvas, text=YLabel,
@@ -230,12 +230,12 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab
 
     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,
-               20),
-           font=labelFont, fill=labelColor)
+        im_drawer.text(
+            text=title,
+            xy=(xLeftOffset + (plotWidth - im_drawer.textsize(
+                title, font=labelFont)[0]) / 2.0,
+                20),
+            font=labelFont, fill=labelColor)
 
 # This function determines the scale of the plot
 
diff --git a/wqflask/utility/__init__.py b/wqflask/utility/__init__.py
index 816bc4df..6c8cd546 100644
--- a/wqflask/utility/__init__.py
+++ b/wqflask/utility/__init__.py
@@ -7,7 +7,7 @@ class Bunch:
     """Like a dictionary but using object notation"""
 
     def __init__(self, **kw):
-            self.__dict__ = kw
+        self.__dict__ = kw
 
     def __repr__(self):
         return pf(self.__dict__)
diff --git a/wqflask/utility/genofile_parser.py b/wqflask/utility/genofile_parser.py
index c0629b5d..eb545478 100644
--- a/wqflask/utility/genofile_parser.py
+++ b/wqflask/utility/genofile_parser.py
@@ -14,87 +14,87 @@ from pprint import pformat as pf
 
 
 class Marker:
-  def __init__(self):
-    self.name = None
-    self.chr = None
-    self.cM = None
-    self.Mb = None
-    self.genotypes = []
+    def __init__(self):
+        self.name = None
+        self.chr = None
+        self.cM = None
+        self.Mb = None
+        self.genotypes = []
 
 
 class ConvertGenoFile:
 
-  def __init__(self, input_file):
-    self.mb_exists = False
-    self.cm_exists = False
-    self.markers = []
+    def __init__(self, input_file):
+        self.mb_exists = False
+        self.cm_exists = False
+        self.markers = []
 
-    self.latest_row_pos = None
-    self.latest_col_pos = None
+        self.latest_row_pos = None
+        self.latest_col_pos = None
 
-    self.latest_row_value = None
-    self.latest_col_value = None
-    self.input_fh = open(input_file)
-    print("!!!!!!!!!!!!!!!!PARSER!!!!!!!!!!!!!!!!!!")
-    self.haplotype_notation = {
-      '@mat': "1",
-      '@pat': "2",
-      '@het': "-999",
-      '@unk': "-999"
-    }
-    self.configurations = {}
+        self.latest_row_value = None
+        self.latest_col_value = None
+        self.input_fh = open(input_file)
+        print("!!!!!!!!!!!!!!!!PARSER!!!!!!!!!!!!!!!!!!")
+        self.haplotype_notation = {
+          '@mat': "1",
+          '@pat': "2",
+          '@het': "-999",
+          '@unk': "-999"
+        }
+        self.configurations = {}
 
-  def process_rows(self):
-    for self.latest_row_pos, row in enumerate(self.input_fh):
-        self.latest_row_value = row
-        # Take care of headers
-        if not row.strip():
-            continue
-        if row.startswith('#'):
-            continue
-        if row.startswith('Chr'):
-            if 'Mb' in row.split():
-                self.mb_exists = True
-            if 'cM' in row.split():
-                self.cm_exists = True
-            skip = 2 + self.cm_exists + self.mb_exists
-            self.individuals = row.split()[skip:]
-            continue
-        if row.startswith('@'):
-            key, _separater, value = row.partition(':')
-            key = key.strip()
-            value = value.strip()
-            if key in self.haplotype_notation:
-                self.configurations[value] = self.haplotype_notation[key]
-            continue
-        if not len(self.configurations):
-            raise EmptyConfigurations
-        yield row
+    def process_rows(self):
+        for self.latest_row_pos, row in enumerate(self.input_fh):
+            self.latest_row_value = row
+            # Take care of headers
+            if not row.strip():
+                continue
+            if row.startswith('#'):
+                continue
+            if row.startswith('Chr'):
+                if 'Mb' in row.split():
+                    self.mb_exists = True
+                if 'cM' in row.split():
+                    self.cm_exists = True
+                skip = 2 + self.cm_exists + self.mb_exists
+                self.individuals = row.split()[skip:]
+                continue
+            if row.startswith('@'):
+                key, _separater, value = row.partition(':')
+                key = key.strip()
+                value = value.strip()
+                if key in self.haplotype_notation:
+                    self.configurations[value] = self.haplotype_notation[key]
+                continue
+            if not len(self.configurations):
+                raise EmptyConfigurations
+            yield row
 
-  def process_csv(self):
-    for row in self.process_rows():
-      row_items = row.split("\t")
+    def process_csv(self):
+        for row in self.process_rows():
+            row_items = row.split("\t")
 
-      this_marker = Marker()
-      this_marker.name = row_items[1]
-      this_marker.chr = row_items[0]
-      if self.cm_exists and self.mb_exists:
-        this_marker.cM = row_items[2]
-        this_marker.Mb = row_items[3]
-        genotypes = row_items[4:]
-      elif self.cm_exists:
-          this_marker.cM = row_items[2]
-          genotypes = row_items[3:]
-      elif self.mb_exists:
-          this_marker.Mb = row_items[2]
-          genotypes = row_items[3:]
-      else:
-        genotypes = row_items[2:]
-      for item_count, genotype in enumerate(genotypes):
-        if genotype.upper().strip() in self.configurations:
-          this_marker.genotypes.append(
-            self.configurations[genotype.upper().strip()])
-        else:
-          print("WARNING:", genotype.upper())
-          this_marker.genotypes.append("NA")
-      self.markers.append(this_marker.__dict__)
+            this_marker = Marker()
+            this_marker.name = row_items[1]
+            this_marker.chr = row_items[0]
+            if self.cm_exists and self.mb_exists:
+                this_marker.cM = row_items[2]
+                this_marker.Mb = row_items[3]
+                genotypes = row_items[4:]
+            elif self.cm_exists:
+                this_marker.cM = row_items[2]
+                genotypes = row_items[3:]
+            elif self.mb_exists:
+                this_marker.Mb = row_items[2]
+                genotypes = row_items[3:]
+            else:
+                genotypes = row_items[2:]
+            for item_count, genotype in enumerate(genotypes):
+                if genotype.upper().strip() in self.configurations:
+                    this_marker.genotypes.append(
+                      self.configurations[genotype.upper().strip()])
+                else:
+                    print("WARNING:", genotype.upper())
+                    this_marker.genotypes.append("NA")
+            self.markers.append(this_marker.__dict__)
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index d82e478d..4f09176a 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -73,7 +73,7 @@ def get_setting(command_id, guess=None):
 def get_setting_bool(id):
     v = get_setting(id)
     if v not in [0, False, 'False', 'FALSE', None]:
-      return True
+        return True
     return False