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authorBonfaceKilz2020-08-19 03:57:05 +0300
committerBonfaceKilz2020-08-19 03:57:05 +0300
commitdb41cd49b6d8ccd2c3318209118ffe098bc9293e (patch)
tree01363468268316fe58335b958c992a9232d6b07e /wqflask
parent3aaa28ea762c496eeb84e09e45194e3fd2a51673 (diff)
downloadgenenetwork2-db41cd49b6d8ccd2c3318209118ffe098bc9293e.tar.gz
Remove extra whitespace(or add it) from comma separated items
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-urllib>
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/base/trait.py6
-rw-r--r--wqflask/db/call.py10
-rw-r--r--wqflask/db/webqtlDatabaseFunction.py8
-rw-r--r--wqflask/maintenance/gen_select_dataset.py2
-rw-r--r--wqflask/maintenance/quantile_normalize.py2
-rw-r--r--wqflask/maintenance/set_resource_defaults.py2
-rw-r--r--wqflask/utility/Plot.py48
-rw-r--r--wqflask/utility/elasticsearch_tools.py2
-rw-r--r--wqflask/utility/logger.py26
-rw-r--r--wqflask/utility/pillow_utils.py4
-rw-r--r--wqflask/utility/startup_config.py2
-rw-r--r--wqflask/utility/svg.py130
-rw-r--r--wqflask/utility/tools.py32
-rw-r--r--wqflask/utility/webqtlUtil.py16
-rw-r--r--wqflask/wqflask/api/router.py8
-rw-r--r--wqflask/wqflask/correlation/show_corr_results.py12
-rw-r--r--wqflask/wqflask/correlation_matrix/show_corr_matrix.py8
-rw-r--r--wqflask/wqflask/do_search.py4
-rw-r--r--wqflask/wqflask/external_tools/send_to_geneweaver.py8
-rw-r--r--wqflask/wqflask/marker_regression/display_mapping_results.py186
-rw-r--r--wqflask/wqflask/marker_regression/plink_mapping.py6
-rw-r--r--wqflask/wqflask/marker_regression/run_mapping.py2
-rw-r--r--wqflask/wqflask/search_results.py2
-rw-r--r--wqflask/wqflask/show_trait/SampleList.py2
-rw-r--r--wqflask/wqflask/user_manager.py2
-rw-r--r--wqflask/wqflask/views.py8
26 files changed, 269 insertions, 269 deletions
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 2b8f2e72..05b272c3 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -193,7 +193,7 @@ class GeneralTrait(object):
'''
if self.chr and self.mb:
- self.location = 'Chr %s @ %s Mb' % (self.chr,self.mb)
+ self.location = 'Chr %s @ %s Mb' % (self.chr, self.mb)
elif self.chr:
self.location = 'Chr %s @ Unknown position' % (self.chr)
else:
@@ -440,7 +440,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
#XZ, 05/08/2009: We also should use Geno.Id to find marker instead of just using Geno.Name
# to avoid the problem of same marker name from different species.
elif dataset.type == 'Geno':
- display_fields_string = string.join(dataset.display_fields,',Geno.')
+ display_fields_string = string.join(dataset.display_fields, ',Geno.')
display_fields_string = 'Geno.' + display_fields_string
query = """
SELECT %s
@@ -459,7 +459,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
query = """SELECT %s FROM %s WHERE Name = %s"""
logger.sql(query)
trait_info = g.db.execute(query,
- (string.join(dataset.display_fields,','),
+ (string.join(dataset.display_fields, ','),
dataset.type, trait.name)).fetchone()
if trait_info:
diff --git a/wqflask/db/call.py b/wqflask/db/call.py
index 82cfebb4..3b8f782e 100644
--- a/wqflask/db/call.py
+++ b/wqflask/db/call.py
@@ -26,8 +26,8 @@ GN_SERVER result when set (which should return a Tuple)
else:
res2 = result,
if LOG_SQL:
- logger.debug("Replaced SQL call",query)
- logger.debug(path,res2)
+ logger.debug("Replaced SQL call", query)
+ logger.debug(path, res2)
return res2
else:
return fetchone(query)
@@ -37,7 +37,7 @@ def fetchone(query):
original fetchone, but with logging)
"""
- with Bench("SQL",LOG_SQL):
+ with Bench("SQL", LOG_SQL):
def helper(query):
res = g.db.execute(query)
return res.fetchone()
@@ -48,7 +48,7 @@ def fetchall(query):
original fetchall, but with logging)
"""
- with Bench("SQL",LOG_SQL):
+ with Bench("SQL", LOG_SQL):
def helper(query):
res = g.db.execute(query)
return res.fetchall()
@@ -58,7 +58,7 @@ def gn_server(path):
"""Return JSON record by calling GN_SERVER
"""
- with Bench("GN_SERVER",LOG_SQL):
+ with Bench("GN_SERVER", LOG_SQL):
res = urllib.request.urlopen(GN_SERVER_URL+path)
rest = res.read()
res2 = json.loads(rest)
diff --git a/wqflask/db/webqtlDatabaseFunction.py b/wqflask/db/webqtlDatabaseFunction.py
index 8a9dc79d..2805febd 100644
--- a/wqflask/db/webqtlDatabaseFunction.py
+++ b/wqflask/db/webqtlDatabaseFunction.py
@@ -35,13 +35,13 @@ def retrieve_species(group):
"""Get the species of a group (e.g. returns string "mouse" on "BXD"
"""
- result = fetch1("select Species.Name from Species, InbredSet where InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id" % (group),"/cross/"+group+".json",lambda r: (r["species"],))[0]
- logger.debug("retrieve_species result:",result)
+ result = fetch1("select Species.Name from Species, InbredSet where InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id" % (group), "/cross/"+group+".json", lambda r: (r["species"],))[0]
+ logger.debug("retrieve_species result:", result)
return result
def retrieve_species_id(group):
- result = fetch1("select SpeciesId from InbredSet where Name = '%s'" % (group),"/cross/"+group+".json",lambda r: (r["species_id"],))[0]
- logger.debug("retrieve_species_id result:",result)
+ result = fetch1("select SpeciesId from InbredSet where Name = '%s'" % (group), "/cross/"+group+".json", lambda r: (r["species_id"],))[0]
+ logger.debug("retrieve_species_id result:", result)
return result
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index 78217587..d12b328f 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -41,7 +41,7 @@ from __future__ import print_function, division
import sys
# NEW: Note we prepend the current path - otherwise a guix instance of GN2 may be used instead
-sys.path.insert(0,'./')
+sys.path.insert(0, './')
# NEW: import app to avoid a circular dependency on utility.tools
from wqflask import app
diff --git a/wqflask/maintenance/quantile_normalize.py b/wqflask/maintenance/quantile_normalize.py
index 82b695f4..43edfd13 100644
--- a/wqflask/maintenance/quantile_normalize.py
+++ b/wqflask/maintenance/quantile_normalize.py
@@ -1,7 +1,7 @@
from __future__ import absolute_import, print_function, division
import sys
-sys.path.insert(0,'./')
+sys.path.insert(0, './')
diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py
index 54fd8e7e..d53a255b 100644
--- a/wqflask/maintenance/set_resource_defaults.py
+++ b/wqflask/maintenance/set_resource_defaults.py
@@ -22,7 +22,7 @@ import sys
import json
# NEW: Note we prepend the current path - otherwise a guix instance of GN2 may be used instead
-sys.path.insert(0,'./')
+sys.path.insert(0, './')
# NEW: import app to avoid a circular dependency on utility.tools
from wqflask import app
diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py
index c9053dde..4f6e694e 100644
--- a/wqflask/utility/Plot.py
+++ b/wqflask/utility/Plot.py
@@ -58,7 +58,7 @@ 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] == '.':
@@ -162,7 +162,7 @@ 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)
@@ -174,7 +174,7 @@ 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
@@ -183,81 +183,81 @@ 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:
@@ -269,7 +269,7 @@ 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)
@@ -287,7 +287,7 @@ 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)))
@@ -296,7 +296,7 @@ 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
diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py
index 15cdd0bc..a5580811 100644
--- a/wqflask/utility/elasticsearch_tools.py
+++ b/wqflask/utility/elasticsearch_tools.py
@@ -59,7 +59,7 @@ def get_elasticsearch_connection(for_user=True):
try:
assert(ELASTICSEARCH_HOST)
assert(ELASTICSEARCH_PORT)
- logger.info("ES HOST",ELASTICSEARCH_HOST)
+ logger.info("ES HOST", ELASTICSEARCH_HOST)
es = Elasticsearch([{
"host": ELASTICSEARCH_HOST, "port": ELASTICSEARCH_PORT
diff --git a/wqflask/utility/logger.py b/wqflask/utility/logger.py
index 510b1041..e904eb94 100644
--- a/wqflask/utility/logger.py
+++ b/wqflask/utility/logger.py
@@ -42,10 +42,10 @@ class GNLogger:
"""
- def __init__(self,name):
+ def __init__(self, name):
self.logger = logging.getLogger(name)
- def setLevel(self,value):
+ def setLevel(self, value):
"""Set the undelying log level"""
self.logger.setLevel(value)
@@ -54,7 +54,7 @@ class GNLogger:
level=num to filter on LOG_LEVEL_DEBUG.
"""
- self.collect(self.logger.debug,*args)
+ self.collect(self.logger.debug, *args)
def debug20(self,*args):
"""Call logging.debug for multiple args. Use level=num to filter on
@@ -63,15 +63,15 @@ LOG_LEVEL_DEBUG (NYI).
"""
if level <= LOG_LEVEL_DEBUG:
if self.logger.getEffectiveLevel() < 20:
- self.collect(self.logger.debug,*args)
+ self.collect(self.logger.debug, *args)
def info(self,*args):
"""Call logging.info for multiple args"""
- self.collect(self.logger.info,*args)
+ self.collect(self.logger.info, *args)
def warning(self,*args):
"""Call logging.warning for multiple args"""
- self.collect(self.logger.warning,*args)
+ self.collect(self.logger.warning, *args)
# self.logger.warning(self.collect(*args))
def error(self,*args):
@@ -79,13 +79,13 @@ LOG_LEVEL_DEBUG (NYI).
now = datetime.datetime.utcnow()
time_str = now.strftime('%H:%M:%S UTC %Y%m%d')
l = [time_str]+list(args)
- self.collect(self.logger.error,*l)
+ self.collect(self.logger.error, *l)
def infof(self,*args):
"""Call logging.info for multiple args lazily"""
# only evaluate function when logging
if self.logger.getEffectiveLevel() < 30:
- self.collectf(self.logger.debug,*args)
+ self.collectf(self.logger.debug, *args)
def debugf(self,level=0,*args):
"""Call logging.debug for multiple args lazily and handle
@@ -95,15 +95,15 @@ LOG_LEVEL_DEBUG (NYI).
# only evaluate function when logging
if level <= LOG_LEVEL_DEBUG:
if self.logger.getEffectiveLevel() < 20:
- self.collectf(self.logger.debug,*args)
+ self.collectf(self.logger.debug, *args)
def sql(self, sqlcommand, fun = None):
"""Log SQL command, optionally invoking a timed fun"""
if LOG_SQL:
caller = stack()[1][3]
- if caller in ['fetchone','fetch1','fetchall']:
+ if caller in ['fetchone', 'fetch1', 'fetchall']:
caller = stack()[2][3]
- self.info(caller,sqlcommand)
+ self.info(caller, sqlcommand)
if fun:
result = fun(sqlcommand)
if LOG_SQL:
@@ -119,7 +119,7 @@ LOG_LEVEL_DEBUG (NYI).
if isinstance(a, str):
out = out + a
else:
- out = out + pf(a,width=160)
+ out = out + pf(a, width=160)
fun(out)
def collectf(self,fun,*args):
@@ -134,7 +134,7 @@ LOG_LEVEL_DEBUG (NYI).
if isinstance(a, str):
out = out + a
else:
- out = out + pf(a,width=160)
+ out = out + pf(a, width=160)
fun(out)
# Get the module logger. You can override log levels at the
diff --git a/wqflask/utility/pillow_utils.py b/wqflask/utility/pillow_utils.py
index dfbf3e19..1e2ed075 100644
--- a/wqflask/utility/pillow_utils.py
+++ b/wqflask/utility/pillow_utils.py
@@ -10,9 +10,9 @@ WHITE = ImageColor.getrgb("white")
def draw_rotated_text(canvas, text, font, xy, fill=BLACK, angle=-90):
# type: (Image, str, ImageFont, tuple, ImageColor, int)
"""Utility function draw rotated text"""
- tmp_img = Image.new("RGBA", font.getsize(text), color=(0,0,0,0))
+ tmp_img = Image.new("RGBA", font.getsize(text), color=(0, 0, 0, 0))
draw_text = ImageDraw.Draw(tmp_img)
- draw_text.text(text=text, xy=(0,0), font=font, fill=fill)
+ draw_text.text(text=text, xy=(0, 0), font=font, fill=fill)
tmp_img2 = tmp_img.rotate(angle, expand=1)
tmp_img2.save("/tmp/{}.png".format(text), format="png")
canvas.paste(im=tmp_img2, box=tuple([int(i) for i in xy]))
diff --git a/wqflask/utility/startup_config.py b/wqflask/utility/startup_config.py
index 42ead709..f1aaebb6 100644
--- a/wqflask/utility/startup_config.py
+++ b/wqflask/utility/startup_config.py
@@ -36,4 +36,4 @@ def app_config():
# import utility.elasticsearch_tools as es
# es.test_elasticsearch_connection()
- print(("GN2 is running. Visit %s[http://localhost:%s/%s](%s)" % (BLUE,str(port),ENDC,get_setting("WEBSERVER_URL"))))
+ print(("GN2 is running. Visit %s[http://localhost:%s/%s](%s)" % (BLUE, str(port), ENDC, get_setting("WEBSERVER_URL"))))
diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py
index 874ada9d..19eda0ce 100644
--- a/wqflask/utility/svg.py
+++ b/wqflask/utility/svg.py
@@ -447,7 +447,7 @@ class rect(SVGelement):
if width == None or height == None:
raise ValueError('both height and width are required')
- SVGelement.__init__(self,'rect',{'width':width,'height':height},**args)
+ SVGelement.__init__(self, 'rect', {'width':width,'height':height}, **args)
if x!=None:
self.attributes['x']=x
if y!=None:
@@ -468,7 +468,7 @@ class ellipse(SVGelement):
if rx==None or ry== None:
raise ValueError('both rx and ry are required')
- SVGelement.__init__(self,'ellipse',{'rx':rx,'ry':ry},**args)
+ SVGelement.__init__(self, 'ellipse', {'rx':rx,'ry':ry}, **args)
if cx!=None:
self.attributes['cx']=cx
if cy!=None:
@@ -489,7 +489,7 @@ class circle(SVGelement):
def __init__(self,cx=None,cy=None,r=None,fill=None,stroke=None,stroke_width=None,**args):
if r==None:
raise ValueError('r is required')
- SVGelement.__init__(self,'circle',{'r':r},**args)
+ SVGelement.__init__(self, 'circle', {'r':r}, **args)
if cx!=None:
self.attributes['cx']=cx
if cy!=None:
@@ -508,7 +508,7 @@ class point(circle):
very small rectangle if you use many points because a circle is difficult to render.
"""
def __init__(self,x,y,fill='black',**args):
- circle.__init__(self,x,y,1,fill,**args)
+ circle.__init__(self, x, y, 1, fill, **args)
class line(SVGelement):
"""l=line(x1,y1,x2,y2,stroke,stroke_width,**args)
@@ -516,7 +516,7 @@ class line(SVGelement):
A line is defined by a begin x,y pair and an end x,y pair
"""
def __init__(self,x1=None,y1=None,x2=None,y2=None,stroke=None,stroke_width=None,**args):
- SVGelement.__init__(self,'line',**args)
+ SVGelement.__init__(self, 'line', **args)
if x1!=None:
self.attributes['x1']=x1
if y1!=None:
@@ -536,7 +536,7 @@ class polyline(SVGelement):
a polyline is defined by a list of xy pairs
"""
def __init__(self,points,fill=None,stroke=None,stroke_width=None,**args):
- SVGelement.__init__(self,'polyline',{'points':_xypointlist(points)},**args)
+ SVGelement.__init__(self, 'polyline', {'points':_xypointlist(points)}, **args)
if fill!=None:
self.attributes['fill']=fill
if stroke_width!=None:
@@ -550,7 +550,7 @@ class polygon(SVGelement):
a polygon is defined by a list of xy pairs
"""
def __init__(self,points,fill=None,stroke=None,stroke_width=None,**args):
- SVGelement.__init__(self,'polygon',{'points':_xypointlist(points)},**args)
+ SVGelement.__init__(self, 'polygon', {'points':_xypointlist(points)}, **args)
if fill!=None:
self.attributes['fill']=fill
if stroke_width!=None:
@@ -564,7 +564,7 @@ class path(SVGelement):
a path is defined by a path object and optional width, stroke and fillcolor
"""
def __init__(self,pathdata,fill=None,stroke=None,stroke_width=None,id=None,**args):
- SVGelement.__init__(self,'path',{'d':str(pathdata)},**args)
+ SVGelement.__init__(self, 'path', {'d':str(pathdata)}, **args)
if stroke!=None:
self.attributes['stroke']=stroke
if fill!=None:
@@ -581,7 +581,7 @@ class text(SVGelement):
a text element can bge used for displaying text on the screen
"""
def __init__(self,x=None,y=None,text=None,font_size=None,font_family=None,text_anchor=None,**args):
- SVGelement.__init__(self,'text',**args)
+ SVGelement.__init__(self, 'text', **args)
if x!=None:
self.attributes['x']=x
if y!=None:
@@ -602,7 +602,7 @@ class textpath(SVGelement):
a textpath places a text on a path which is referenced by a link.
"""
def __init__(self,link,text=None,**args):
- SVGelement.__init__(self,'textPath',{'xlink:href':link},**args)
+ SVGelement.__init__(self, 'textPath', {'xlink:href':link}, **args)
if text!=None:
self.text=text
@@ -614,7 +614,7 @@ class pattern(SVGelement):
in x and y to cover the areas to be painted.
"""
def __init__(self,x=None,y=None,width=None,height=None,patternUnits=None,**args):
- SVGelement.__init__(self,'pattern',**args)
+ SVGelement.__init__(self, 'pattern', **args)
if x!=None:
self.attributes['x']=x
if y!=None:
@@ -633,7 +633,7 @@ class title(SVGelement):
add at least one to the root svg element
"""
def __init__(self,text=None,**args):
- SVGelement.__init__(self,'title',**args)
+ SVGelement.__init__(self, 'title', **args)
if text!=None:
self.text=text
@@ -644,7 +644,7 @@ class description(SVGelement):
Add this element before adding other elements.
"""
def __init__(self,text=None,**args):
- SVGelement.__init__(self,'desc',**args)
+ SVGelement.__init__(self, 'desc', **args)
if text!=None:
self.text=text
@@ -655,7 +655,7 @@ class lineargradient(SVGelement):
stop elements van be added to define the gradient colors.
"""
def __init__(self,x1=None,y1=None,x2=None,y2=None,id=None,**args):
- SVGelement.__init__(self,'linearGradient',**args)
+ SVGelement.__init__(self, 'linearGradient', **args)
if x1!=None:
self.attributes['x1']=x1
if y1!=None:
@@ -674,7 +674,7 @@ class radialgradient(SVGelement):
stop elements van be added to define the gradient colors.
"""
def __init__(self,cx=None,cy=None,r=None,fx=None,fy=None,id=None,**args):
- SVGelement.__init__(self,'radialGradient',**args)
+ SVGelement.__init__(self, 'radialGradient', **args)
if cx!=None:
self.attributes['cx']=cx
if cy!=None:
@@ -694,7 +694,7 @@ class stop(SVGelement):
Puts a stop color at the specified radius
"""
def __init__(self,offset,stop_color=None,**args):
- SVGelement.__init__(self,'stop',{'offset':offset},**args)
+ SVGelement.__init__(self, 'stop', {'offset':offset}, **args)
if stop_color!=None:
self.attributes['stop-color']=stop_color
@@ -704,7 +704,7 @@ class style(SVGelement):
Add a CDATA element to this element for defing in line stylesheets etc..
"""
def __init__(self,type,cdata=None,**args):
- SVGelement.__init__(self,'style',{'type':type},cdata=cdata, **args)
+ SVGelement.__init__(self, 'style', {'type':type}, cdata=cdata, **args)
class image(SVGelement):
@@ -715,7 +715,7 @@ class image(SVGelement):
def __init__(self,url,x=None,y=None,width=None,height=None,**args):
if width==None or height==None:
raise ValueError('both height and width are required')
- SVGelement.__init__(self,'image',{'xlink:href':url,'width':width,'height':height},**args)
+ SVGelement.__init__(self, 'image', {'xlink:href':url,'width':width,'height':height}, **args)
if x!=None:
self.attributes['x']=x
if y!=None:
@@ -727,7 +727,7 @@ class cursor(SVGelement):
defines a custom cursor for a element or a drawing
"""
def __init__(self,url,**args):
- SVGelement.__init__(self,'cursor',{'xlink:href':url},**args)
+ SVGelement.__init__(self, 'cursor', {'xlink:href':url}, **args)
class marker(SVGelement):
@@ -737,7 +737,7 @@ class marker(SVGelement):
add an element to it which should be used as a marker.
"""
def __init__(self,id=None,viewBox=None,refx=None,refy=None,markerWidth=None,markerHeight=None,**args):
- SVGelement.__init__(self,'marker',**args)
+ SVGelement.__init__(self, 'marker', **args)
if id!=None:
self.attributes['id']=id
if viewBox!=None:
@@ -758,7 +758,7 @@ class group(SVGelement):
g.addElement(SVGelement)
"""
def __init__(self,id=None,**args):
- SVGelement.__init__(self,'g',**args)
+ SVGelement.__init__(self, 'g', **args)
if id!=None:
self.attributes['id']=id
@@ -772,7 +772,7 @@ class symbol(SVGelement):
"""
def __init__(self,id=None,viewBox=None,**args):
- SVGelement.__init__(self,'symbol',**args)
+ SVGelement.__init__(self, 'symbol', **args)
if id!=None:
self.attributes['id']=id
if viewBox!=None:
@@ -784,7 +784,7 @@ class defs(SVGelement):
container for defining elements
"""
def __init__(self,**args):
- SVGelement.__init__(self,'defs',**args)
+ SVGelement.__init__(self, 'defs', **args)
class switch(SVGelement):
"""sw=switch(**args)
@@ -794,7 +794,7 @@ class switch(SVGelement):
Refer to the SVG specification for details.
"""
def __init__(self,**args):
- SVGelement.__init__(self,'switch',**args)
+ SVGelement.__init__(self, 'switch', **args)
class use(SVGelement):
@@ -803,7 +803,7 @@ class use(SVGelement):
references a symbol by linking to its id and its position, height and width
"""
def __init__(self,link,x=None,y=None,width=None,height=None,**args):
- SVGelement.__init__(self,'use',{'xlink:href':link},**args)
+ SVGelement.__init__(self, 'use', {'xlink:href':link}, **args)
if x!=None:
self.attributes['x']=x
if y!=None:
@@ -822,14 +822,14 @@ class link(SVGelement):
a.addElement(SVGelement)
"""
def __init__(self,link='',**args):
- SVGelement.__init__(self,'a',{'xlink:href':link},**args)
+ SVGelement.__init__(self, 'a', {'xlink:href':link}, **args)
class view(SVGelement):
"""v=view(id,**args)
a view can be used to create a view with different attributes"""
def __init__(self,id=None,**args):
- SVGelement.__init__(self,'view',**args)
+ SVGelement.__init__(self, 'view', **args)
if id!=None:
self.attributes['id']=id
@@ -840,7 +840,7 @@ class script(SVGelement):
"""
def __init__(self,type,cdata=None,**args):
- SVGelement.__init__(self,'script',{'type':type},cdata=cdata,**args)
+ SVGelement.__init__(self, 'script', {'type':type}, cdata=cdata, **args)
class animate(SVGelement):
"""an=animate(attribute,from,to,during,**args)
@@ -848,7 +848,7 @@ class animate(SVGelement):
animates an attribute.
"""
def __init__(self,attribute,fr=None,to=None,dur=None,**args):
- SVGelement.__init__(self,'animate',{'attributeName':attribute},**args)
+ SVGelement.__init__(self, 'animate', {'attributeName':attribute}, **args)
if fr!=None:
self.attributes['from']=fr
if to!=None:
@@ -862,7 +862,7 @@ class animateMotion(SVGelement):
animates a SVGelement over the given path in dur seconds
"""
def __init__(self,pathdata,dur,**args):
- SVGelement.__init__(self,'animateMotion',**args)
+ SVGelement.__init__(self, 'animateMotion', **args)
if pathdata!=None:
self.attributes['path']=str(pathdata)
if dur!=None:
@@ -874,7 +874,7 @@ class animateTransform(SVGelement):
transform an element from and to a value.
"""
def __init__(self,type=None,fr=None,to=None,dur=None,**args):
- SVGelement.__init__(self,'animateTransform',{'attributeName':'transform'},**args)
+ SVGelement.__init__(self, 'animateTransform', {'attributeName':'transform'}, **args)
# As far as I know the attributeName is always transform
if type!=None:
self.attributes['type']=type
@@ -890,7 +890,7 @@ class animateColor(SVGelement):
Animates the color of a element
"""
def __init__(self,attribute,type=None,fr=None,to=None,dur=None,**args):
- SVGelement.__init__(self,'animateColor',{'attributeName':attribute},**args)
+ SVGelement.__init__(self, 'animateColor', {'attributeName':attribute}, **args)
if type!=None:
self.attributes['type']=type
if fr!=None:
@@ -905,7 +905,7 @@ class set(SVGelement):
sets an attribute to a value for a
"""
def __init__(self,attribute,to=None,dur=None,**args):
- SVGelement.__init__(self,'set',{'attributeName':attribute},**args)
+ SVGelement.__init__(self, 'set', {'attributeName':attribute}, **args)
if to!=None:
self.attributes['to']=to
if dur!=None:
@@ -929,7 +929,7 @@ class svg(SVGelement):
d.toXml()
"""
def __init__(self,viewBox=None, width=None, height=None,**args):
- SVGelement.__init__(self,'svg',**args)
+ SVGelement.__init__(self, 'svg', **args)
if viewBox!=None:
self.attributes['viewBox']=_viewboxlist(viewBox)
if width!=None:
@@ -952,7 +952,7 @@ class drawing:
def __init__(self, entity={}):
self.svg=None
self.entity = entity
- def setSVG(self,svg):
+ def setSVG(self, svg):
self.svg=svg
# Voeg een element toe aan de grafiek toe.
if use_dom_implementation==0:
@@ -967,12 +967,12 @@ class drawing:
xml.write("<!ENTITY %s \"%s\">\n" % (item, self.entity[item]))
xml.write("]")
xml.write(">\n")
- self.svg.toXml(0,xml)
+ self.svg.toXml(0, xml)
if not filename:
if compress:
import gzip
f=cStringIO.StringIO()
- zf=gzip.GzipFile(fileobj=f,mode='wb')
+ zf=gzip.GzipFile(fileobj=f, mode='wb')
zf.write(xml.getvalue())
zf.close()
f.seek(0)
@@ -982,11 +982,11 @@ class drawing:
else:
if filename[-4:]=='svgz':
import gzip
- f=gzip.GzipFile(filename=filename,mode="wb", compresslevel=9)
+ f=gzip.GzipFile(filename=filename, mode="wb", compresslevel=9)
f.write(xml.getvalue())
f.close()
else:
- f=file(filename,'w')
+ f=file(filename, 'w')
f.write(xml.getvalue())
f.close()
@@ -997,40 +997,40 @@ class drawing:
writes a svg drawing to the screen or to a file
compresses if filename ends with svgz or if compress is true
"""
- doctype = implementation.createDocumentType('svg',"-//W3C//DTD SVG 1.0//EN""",'http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd ')
+ doctype = implementation.createDocumentType('svg', "-//W3C//DTD SVG 1.0//EN""", 'http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd ')
global root
# root is defined global so it can be used by the appender. Its also possible to use it as an arugument but
# that is a bit messy.
- root=implementation.createDocument(None,None,doctype)
+ root=implementation.createDocument(None, None, doctype)
# Create the xml document.
global appender
- def appender(element,elementroot):
+ def appender(element, elementroot):
"""This recursive function appends elements to an element and sets the attributes
and type. It stops when alle elements have been appended"""
if element.namespace:
- e=root.createElementNS(element.namespace,element.type)
+ e=root.createElementNS(element.namespace, element.type)
else:
e=root.createElement(element.type)
if element.text:
textnode=root.createTextNode(element.text)
e.appendChild(textnode)
for attribute in list(element.attributes.keys()): #in element.attributes is supported from python 2.2
- e.setAttribute(attribute,str(element.attributes[attribute]))
+ e.setAttribute(attribute, str(element.attributes[attribute]))
if element.elements:
for el in element.elements:
- e=appender(el,e)
+ e=appender(el, e)
elementroot.appendChild(e)
return elementroot
- root=appender(self.svg,root)
+ root=appender(self.svg, root)
if not filename:
import cStringIO
xml=cStringIO.StringIO()
- PrettyPrint(root,xml)
+ PrettyPrint(root, xml)
if compress:
import gzip
f=cStringIO.StringIO()
- zf=gzip.GzipFile(fileobj=f,mode='wb')
+ zf=gzip.GzipFile(fileobj=f, mode='wb')
zf.write(xml.getvalue())
zf.close()
f.seek(0)
@@ -1043,13 +1043,13 @@ class drawing:
import gzip
import cStringIO
xml=cStringIO.StringIO()
- PrettyPrint(root,xml)
- f=gzip.GzipFile(filename=filename,mode='wb',compresslevel=9)
+ PrettyPrint(root, xml)
+ f=gzip.GzipFile(filename=filename, mode='wb', compresslevel=9)
f.write(xml.getvalue())
f.close()
else:
- f=open(filename,'w')
- PrettyPrint(root,f)
+ f=open(filename, 'w')
+ PrettyPrint(root, f)
f.close()
except:
print(("Cannot write SVG file: " + filename))
@@ -1070,32 +1070,32 @@ if __name__=='__main__':
d=drawing()
- s=svg((0,0,100,100))
- r=rect(-100,-100,300,300,'cyan')
+ s=svg((0, 0, 100, 100))
+ r=rect(-100, -100, 300, 300, 'cyan')
s.addElement(r)
t=title('SVGdraw Demo')
s.addElement(t)
g=group('animations')
- e=ellipse(0,0,5,2)
+ e=ellipse(0, 0, 5, 2)
g.addElement(e)
- c=circle(0,0,1,'red')
+ c=circle(0, 0, 1, 'red')
g.addElement(c)
- pd=pathdata(0,-10)
+ pd=pathdata(0, -10)
for i in range(6):
- pd.relsmbezier(10,5,0,10)
- pd.relsmbezier(-10,5,0,10)
- an=animateMotion(pd,10)
+ pd.relsmbezier(10, 5, 0, 10)
+ pd.relsmbezier(-10, 5, 0, 10)
+ an=animateMotion(pd, 10)
an.attributes['rotate']='auto-reverse'
an.attributes['repeatCount']="indefinite"
g.addElement(an)
s.addElement(g)
- for i in range(20,120,20):
- u=use('#animations',i,0)
+ for i in range(20, 120, 20):
+ u=use('#animations', i, 0)
s.addElement(u)
- for i in range(0,120,20):
- for j in range(5,105,10):
- c=circle(i,j,1,'red','black',.5)
+ for i in range(0, 120, 20):
+ for j in range(5, 105, 10):
+ c=circle(i, j, 1, 'red', 'black', .5)
s.addElement(c)
d.setSVG(s)
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 51a87fe1..68ef0f04 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -15,7 +15,7 @@ OVERRIDES = {}
def app_set(command_id, value):
"""Set application wide value"""
- app.config.setdefault(command_id,value)
+ app.config.setdefault(command_id, value)
return value
def get_setting(command_id,guess=None):
@@ -45,7 +45,7 @@ def get_setting(command_id,guess=None):
def value(command):
if command:
# sys.stderr.write("Found "+command+"\n")
- app_set(command_id,command)
+ app_set(command_id, command)
return command
else:
return None
@@ -68,7 +68,7 @@ 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]:
+ if v not in [0, False, 'False', 'FALSE', None]:
return True
return False
@@ -108,16 +108,16 @@ def js_path(module=None):
raise "No JS path found for "+module+" (if not in Guix check JS_GN_PATH)"
def reaper_command(guess=None):
- return get_setting("REAPER_COMMAND",guess)
+ return get_setting("REAPER_COMMAND", guess)
def gemma_command(guess=None):
- return assert_bin(get_setting("GEMMA_COMMAND",guess))
+ return assert_bin(get_setting("GEMMA_COMMAND", guess))
def gemma_wrapper_command(guess=None):
- return assert_bin(get_setting("GEMMA_WRAPPER_COMMAND",guess))
+ return assert_bin(get_setting("GEMMA_WRAPPER_COMMAND", guess))
def plink_command(guess=None):
- return assert_bin(get_setting("PLINK_COMMAND",guess))
+ return assert_bin(get_setting("PLINK_COMMAND", guess))
def flat_file_exists(subdir):
base = get_setting("GENENETWORK_FILES")
@@ -180,7 +180,7 @@ def locate(name, subdir=None):
raise Exception("Can not locate "+name+" in "+base)
def locate_phewas(name, subdir=None):
- return locate(name,'/phewas/'+subdir)
+ return locate(name, '/phewas/'+subdir)
def locate_ignore_error(name, subdir=None):
"""
@@ -204,7 +204,7 @@ def tempdir():
"""
Get UNIX TMPDIR by default
"""
- return valid_path(get_setting("TMPDIR","/tmp"))
+ return valid_path(get_setting("TMPDIR", "/tmp"))
BLUE = '\033[94m'
GREEN = '\033[92m'
@@ -225,9 +225,9 @@ def show_settings():
keylist.sort()
for k in keylist:
try:
- print(("%s: %s%s%s%s" % (k,BLUE,BOLD,get_setting(k),ENDC)))
+ print(("%s: %s%s%s%s" % (k, BLUE, BOLD, get_setting(k), ENDC)))
except:
- print(("%s: %s%s%s%s" % (k,GREEN,BOLD,app.config[k],ENDC)))
+ print(("%s: %s%s%s%s" % (k, GREEN, BOLD, app.config[k], ENDC)))
# Cached values
@@ -279,10 +279,10 @@ SMTP_CONNECT = get_setting('SMTP_CONNECT')
SMTP_USERNAME = get_setting('SMTP_USERNAME')
SMTP_PASSWORD = get_setting('SMTP_PASSWORD')
-REAPER_COMMAND = app_set("REAPER_COMMAND",reaper_command())
-GEMMA_COMMAND = app_set("GEMMA_COMMAND",gemma_command())
+REAPER_COMMAND = app_set("REAPER_COMMAND", reaper_command())
+GEMMA_COMMAND = app_set("GEMMA_COMMAND", gemma_command())
assert(GEMMA_COMMAND is not None)
-PLINK_COMMAND = app_set("PLINK_COMMAND",plink_command())
+PLINK_COMMAND = app_set("PLINK_COMMAND", plink_command())
GEMMA_WRAPPER_COMMAND = gemma_wrapper_command()
TEMPDIR = tempdir() # defaults to UNIX TMPDIR
assert_dir(TEMPDIR)
@@ -295,11 +295,11 @@ assert_dir(JS_GUIX_PATH+'/cytoscape-panzoom')
CSS_PATH = JS_GUIX_PATH # The CSS is bundled together with the JS
# assert_dir(JS_PATH)
-JS_TWITTER_POST_FETCHER_PATH = get_setting("JS_TWITTER_POST_FETCHER_PATH",js_path("javascript-twitter-post-fetcher"))
+JS_TWITTER_POST_FETCHER_PATH = get_setting("JS_TWITTER_POST_FETCHER_PATH", js_path("javascript-twitter-post-fetcher"))
assert_dir(JS_TWITTER_POST_FETCHER_PATH)
assert_file(JS_TWITTER_POST_FETCHER_PATH+"/js/twitterFetcher_min.js")
-JS_CYTOSCAPE_PATH = get_setting("JS_CYTOSCAPE_PATH",js_path("cytoscape"))
+JS_CYTOSCAPE_PATH = get_setting("JS_CYTOSCAPE_PATH", js_path("cytoscape"))
assert_dir(JS_CYTOSCAPE_PATH)
assert_file(JS_CYTOSCAPE_PATH+'/cytoscape.min.js')
diff --git a/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py
index 79991149..77cc3416 100644
--- a/wqflask/utility/webqtlUtil.py
+++ b/wqflask/utility/webqtlUtil.py
@@ -41,22 +41,22 @@ ParInfo ={
'C57BL-6JxC57BL-6NJF2':['', '', 'C57BL/6J', 'C57BL/6NJ'],
'BXD300':['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
'B6BTBRF2':['B6BTBRF1', 'BTBRB6F1', 'C57BL/6J', 'BTBRT<+>tf/J'],
-'BHHBF2':['B6HF2','HB6F2','C57BL/6J','C3H/HeJ'],
-'BHF2':['B6HF2','HB6F2','C57BL/6J','C3H/HeJ'],
+'BHHBF2':['B6HF2', 'HB6F2', 'C57BL/6J', 'C3H/HeJ'],
+'BHF2':['B6HF2', 'HB6F2', 'C57BL/6J', 'C3H/HeJ'],
'B6D2F2':['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
'BDF2-1999':['B6D2F2', 'D2B6F2', 'C57BL/6J', 'DBA/2J'],
'BDF2-2005':['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
-'CTB6F2':['CTB6F2','B6CTF2','C57BL/6J','Castaneous'],
+'CTB6F2':['CTB6F2', 'B6CTF2', 'C57BL/6J', 'Castaneous'],
'CXB':['CBF1', 'BCF1', 'C57BL/6ByJ', 'BALB/cByJ'],
'AXBXA':['ABF1', 'BAF1', 'C57BL/6J', 'A/J'],
'AXB':['ABF1', 'BAF1', 'C57BL/6J', 'A/J'],
'BXA':['BAF1', 'ABF1', 'C57BL/6J', 'A/J'],
'LXS':['LSF1', 'SLF1', 'ISS', 'ILS'],
'HXBBXH':['SHR_BNF1', 'BN_SHRF1', 'BN-Lx/Cub', 'SHR/OlaIpcv'],
-'BayXSha':['BayXShaF1', 'ShaXBayF1', 'Bay-0','Shahdara'],
-'ColXBur':['ColXBurF1', 'BurXColF1', 'Col-0','Bur-0'],
-'ColXCvi':['ColXCviF1', 'CviXColF1', 'Col-0','Cvi'],
-'SXM':['SMF1', 'MSF1', 'Steptoe','Morex'],
+'BayXSha':['BayXShaF1', 'ShaXBayF1', 'Bay-0', 'Shahdara'],
+'ColXBur':['ColXBurF1', 'BurXColF1', 'Col-0', 'Bur-0'],
+'ColXCvi':['ColXCviF1', 'CviXColF1', 'Col-0', 'Cvi'],
+'SXM':['SMF1', 'MSF1', 'Steptoe', 'Morex'],
'HRDP':['SHR_BNF1', 'BN_SHRF1', 'BN-Lx/Cub', 'SHR/OlaIpcv']
}
@@ -91,7 +91,7 @@ def readLineCSV(line): ### dcrowell July 2008
returnList[0]=returnList[0][1:]
return returnList
-def cmpEigenValue(A,B):
+def cmpEigenValue(A, B):
try:
if A[0] > B[0]:
return -1
diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py
index 3fa1d5ba..b81da0dc 100644
--- a/wqflask/wqflask/api/router.py
+++ b/wqflask/wqflask/api/router.py
@@ -558,10 +558,10 @@ def trait_sample_data(dataset_name, trait_name, file_format = "json"):
sample_list = []
for sample in sample_data:
sample_dict = {
- "sample_name" : sample[0],
- "sample_name_2" : sample[1],
- "value" : sample[2],
- "data_id" : sample[3],
+ "sample_name": sample[0],
+ "sample_name_2": sample[1],
+ "value": sample[2],
+ "data_id": sample[3],
}
if sample[4]:
sample_dict["se"] = sample[4]
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 15a21ee6..4116e2df 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -108,17 +108,17 @@ class CorrelationResults(object):
self.sample_data = {}
self.corr_type = start_vars['corr_type']
self.corr_method = start_vars['corr_sample_method']
- self.min_expr = get_float(start_vars,'min_expr')
- self.p_range_lower = get_float(start_vars,'p_range_lower',-1.0)
- self.p_range_upper = get_float(start_vars,'p_range_upper',1.0)
+ self.min_expr = get_float(start_vars, 'min_expr')
+ self.p_range_lower = get_float(start_vars, 'p_range_lower', -1.0)
+ self.p_range_upper = get_float(start_vars, 'p_range_upper', 1.0)
if ('loc_chr' in start_vars and
'min_loc_mb' in start_vars and
'max_loc_mb' in start_vars):
- self.location_chr = get_string(start_vars,'loc_chr')
- self.min_location_mb = get_int(start_vars,'min_loc_mb')
- self.max_location_mb = get_int(start_vars,'max_loc_mb')
+ self.location_chr = get_string(start_vars, 'loc_chr')
+ self.min_location_mb = get_int(start_vars, 'min_loc_mb')
+ self.max_location_mb = get_int(start_vars, 'max_loc_mb')
else:
self.location_chr = self.min_location_mb = self.max_location_mb = None
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index 832746bb..b582cd23 100644
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -275,8 +275,8 @@ def zScore(trait_data_array):
i = 0
for data in trait_data_array:
N = len(data)
- S = reduce(lambda x,y: x+y, data, 0.)
- SS = reduce(lambda x,y: x+y*y, data, 0.)
+ S = reduce(lambda x, y: x+y, data, 0.)
+ SS = reduce(lambda x, y: x+y*y, data, 0.)
mean = S/N
var = SS - S*S/N
stdev = math.sqrt(var/(N-1))
@@ -294,7 +294,7 @@ def sortEigenVectors(vector):
combines = []
i = 0
for item in eigenValues:
- combines.append([eigenValues[i],eigenVectors[i]])
+ combines.append([eigenValues[i], eigenVectors[i]])
i += 1
combines.sort(webqtlUtil.cmpEigenValue)
A = []
@@ -302,7 +302,7 @@ def sortEigenVectors(vector):
for item in combines:
A.append(item[0])
B.append(item[1])
- sum = reduce(lambda x,y: x+y, A, 0.0)
+ sum = reduce(lambda x, y: x+y, A, 0.0)
A = [x*100.0/sum for x in A]
return [A, B]
except:
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index 1e15d28f..cc9c1860 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -46,8 +46,8 @@ class DoSearch(object):
def handle_wildcard(self, str):
keyword = str.strip()
- keyword = keyword.replace("*",".*")
- keyword = keyword.replace("?",".")
+ keyword = keyword.replace("*", ".*")
+ keyword = keyword.replace("?", ".")
return keyword
diff --git a/wqflask/wqflask/external_tools/send_to_geneweaver.py b/wqflask/wqflask/external_tools/send_to_geneweaver.py
index 7a5dba73..9844bab4 100644
--- a/wqflask/wqflask/external_tools/send_to_geneweaver.py
+++ b/wqflask/wqflask/external_tools/send_to_geneweaver.py
@@ -54,10 +54,10 @@ class SendToGeneWeaver(object):
trait_name_list = get_trait_name_list(self.trait_list)
self.hidden_vars = {
- 'client' : "genenetwork",
- 'species' : species_name,
- 'idtype' : self.chip_name,
- 'list' : string.join(trait_name_list, ","),
+ 'client': "genenetwork",
+ 'species': species_name,
+ 'idtype': self.chip_name,
+ 'list': string.join(trait_name_list, ","),
}
def get_trait_name_list(trait_list):
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index c8b9c405..f282b010 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -27,8 +27,8 @@
import datetime
import string
from math import *
-from PIL import (Image,ImageDraw,ImageFont,ImageColor)
-import sys,os
+from PIL import (Image, ImageDraw, ImageFont, ImageColor)
+import sys, os
import cPickle
import httplib
import json
@@ -426,7 +426,7 @@ class DisplayMappingResults(object):
else:
continue
samplelist = list(self.genotype.prgy)
- for j,_geno in enumerate (self.genotype[0][1].genotype):
+ for j, _geno in enumerate (self.genotype[0][1].genotype):
for item in smd:
if item.name == samplelist[j]:
self.NR_INDIVIDUALS = self.NR_INDIVIDUALS + 1
@@ -518,7 +518,7 @@ class DisplayMappingResults(object):
#Scales plot differently for high resolution
if self.draw2X:
- intCanvasX2 = Image.new("RGBA", size=(self.graphWidth*2,self.graphHeight*2))
+ intCanvasX2 = Image.new("RGBA", size=(self.graphWidth*2, self.graphHeight*2))
gifmapX2 = self.plotIntMapping(intCanvasX2, startMb = self.startMb, endMb = self.endMb, showLocusForm= showLocusForm, zoom=2)
intCanvasX2.save(
"{}.png".format(
@@ -745,17 +745,17 @@ class DisplayMappingResults(object):
bootScale = bootScale[:-1] + [highestPercent]
bootOffset = 50*fontZoom
- bootScaleFont=ImageFont.truetype(font=VERDANA_FILE,size=13*fontZoom)
+ bootScaleFont=ImageFont.truetype(font=VERDANA_FILE, size=13*fontZoom)
im_drawer.rectangle(
xy=((canvas.size[0]-bootOffset, yZero-bootHeightThresh),
- (canvas.size[0]-bootOffset-15*zoom,yZero)),
+ (canvas.size[0]-bootOffset-15*zoom, yZero)),
fill = YELLOW, outline=BLACK)
im_drawer.line(
xy=((canvas.size[0]-bootOffset+4, yZero),
(canvas.size[0]-bootOffset, yZero)),
fill=BLACK)
TEXT_Y_DISPLACEMENT = -8
- im_drawer.text(xy=(canvas.size[0]-bootOffset+10,yZero+TEXT_Y_DISPLACEMENT), text='0%',
+ im_drawer.text(xy=(canvas.size[0]-bootOffset+10, yZero+TEXT_Y_DISPLACEMENT), text='0%',
font=bootScaleFont, fill=BLACK)
for item in bootScale:
@@ -763,10 +763,10 @@ class DisplayMappingResults(object):
continue
bootY = yZero-bootHeightThresh*item/highestPercent
im_drawer.line(
- xy=((canvas.size[0]-bootOffset+4,bootY),
- (canvas.size[0]-bootOffset,bootY)),
+ xy=((canvas.size[0]-bootOffset+4, bootY),
+ (canvas.size[0]-bootOffset, bootY)),
fill=BLACK)
- im_drawer.text(xy=(canvas.size[0]-bootOffset+10,bootY+TEXT_Y_DISPLACEMENT),
+ im_drawer.text(xy=(canvas.size[0]-bootOffset+10, bootY+TEXT_Y_DISPLACEMENT),
text='%2.1f'%item, font=bootScaleFont, fill=BLACK)
if self.legendChecked:
@@ -775,7 +775,7 @@ class DisplayMappingResults(object):
smallLabelFont = ImageFont.truetype(font=TREBUC_FILE, size=12*fontZoom)
leftOffset = xLeftOffset+(nCol-1)*200
im_drawer.rectangle(
- xy=((leftOffset,startPosY-6), (leftOffset+12,startPosY+6)),
+ xy=((leftOffset, startPosY-6), (leftOffset+12, startPosY+6)),
fill=YELLOW, outline=BLACK)
im_drawer.text(xy=(leftOffset+ 20, startPosY+TEXT_Y_DISPLACEMENT),
text='Frequency of the Peak LRS',
@@ -872,7 +872,7 @@ class DisplayMappingResults(object):
TEXT_Y_DISPLACEMENT = -8
im_drawer.text(
text="Sequence Site",
- xy=(leftOffset+15,startPosY+TEXT_Y_DISPLACEMENT), font=smallLabelFont,
+ xy=(leftOffset+15, startPosY+TEXT_Y_DISPLACEMENT), font=smallLabelFont,
fill=self.TOP_RIGHT_INFO_COLOR)
def drawSNPTrackNew(self, canvas, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
@@ -922,7 +922,7 @@ class DisplayMappingResults(object):
def drawMultiTraitName(self, fd, canvas, gifmap, showLocusForm, offset= (40, 120, 80, 10), zoom = 1):
nameWidths = []
yPaddingTop = 10
- colorFont=ImageFont.truetype(font=TREBUC_FILE,size=12)
+ colorFont=ImageFont.truetype(font=TREBUC_FILE, size=12)
if len(self.qtlresults) >20 and self.selectedChr > -1:
rightShift = 20
rightShiftStep = 60
@@ -941,20 +941,20 @@ class DisplayMappingResults(object):
rightShift += rightShiftStep
name = thisTrait.displayName()
- nameWidth, nameHeight = im_drawer.textsize(name,font=colorFont)
+ nameWidth, nameHeight = im_drawer.textsize(name, font=colorFont)
nameWidths.append(nameWidth)
im_drawer.rectangle(
- xy=((rightShift,yPaddingTop+kstep*15),
- (rectWidth+rightShift,yPaddingTop+10+kstep*15)),
+ xy=((rightShift, yPaddingTop+kstep*15),
+ (rectWidth+rightShift, yPaddingTop+10+kstep*15)),
fill=thisLRSColor, outline=BLACK)
im_drawer.text(
- text=name,xy=(rectWidth+2+rightShift,yPaddingTop+10+kstep*15),
- font=colorFont,fill=BLACK)
+ text=name, xy=(rectWidth+2+rightShift, yPaddingTop+10+kstep*15),
+ font=colorFont, fill=BLACK)
if thisTrait.db:
- COORDS = "%d,%d,%d,%d" %(rectWidth+2+rightShift,yPaddingTop+kstep*15,rectWidth+2+rightShift+nameWidth,yPaddingTop+10+kstep*15,)
+ COORDS = "%d,%d,%d,%d" %(rectWidth+2+rightShift, yPaddingTop+kstep*15, rectWidth+2+rightShift+nameWidth, yPaddingTop+10+kstep*15,)
HREF= "javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm, thisTrait.db.name, thisTrait.name)
- Areas = HT.Area(shape='rect',coords=COORDS,href=HREF)
+ Areas = HT.Area(shape='rect', coords=COORDS, href=HREF)
gifmap.areas.append(Areas)
def drawLegendPanel(self, canvas, offset= (40, 120, 80, 10), zoom = 1):
@@ -968,80 +968,80 @@ class DisplayMappingResults(object):
if zoom == 2:
fontZoom = 1.5
- labelFont=ImageFont.truetype(font=TREBUC_FILE,size=12*fontZoom)
+ labelFont=ImageFont.truetype(font=TREBUC_FILE, size=12*fontZoom)
startPosY = 15
stepPosY = 12*fontZoom
if self.manhattan_plot != True:
im_drawer.line(
- xy=((xLeftOffset,startPosY),(xLeftOffset+32,startPosY)),
+ xy=((xLeftOffset, startPosY), (xLeftOffset+32, startPosY)),
fill=self.LRS_COLOR, width=2)
im_drawer.text(
- text=self.LRS_LOD, xy=(xLeftOffset+40,startPosY+TEXT_Y_DISPLACEMENT),
- font=labelFont,fill=BLACK)
+ text=self.LRS_LOD, xy=(xLeftOffset+40, startPosY+TEXT_Y_DISPLACEMENT),
+ font=labelFont, fill=BLACK)
startPosY += stepPosY
if self.additiveChecked:
startPosX = xLeftOffset
im_drawer.line(
- xy=((startPosX,startPosY),(startPosX+17,startPosY)),
+ xy=((startPosX, startPosY), (startPosX+17, startPosY)),
fill=self.ADDITIVE_COLOR_POSITIVE, width=2)
im_drawer.line(
- xy=((startPosX+18,startPosY),(startPosX+32,startPosY)),
+ xy=((startPosX+18, startPosY), (startPosX+32, startPosY)),
fill=self.ADDITIVE_COLOR_NEGATIVE, width=2)
im_drawer.text(
- text='Additive Effect',xy=(startPosX+40,startPosY+TEXT_Y_DISPLACEMENT),
- font=labelFont,fill=BLACK)
+ text='Additive Effect', xy=(startPosX+40, startPosY+TEXT_Y_DISPLACEMENT),
+ font=labelFont, fill=BLACK)
if self.genotype.type == 'intercross' and self.dominanceChecked:
startPosX = xLeftOffset
startPosY += stepPosY
im_drawer.line(
- xy=((startPosX,startPosY),(startPosX+17,startPosY)),
+ xy=((startPosX, startPosY), (startPosX+17, startPosY)),
fill=self.DOMINANCE_COLOR_POSITIVE, width=4)
im_drawer.line(
- xy=((startPosX+18,startPosY),(startPosX+35,startPosY)),
+ xy=((startPosX+18, startPosY), (startPosX+35, startPosY)),
fill=self.DOMINANCE_COLOR_NEGATIVE, width=4)
im_drawer.text(
- text='Dominance Effect', xy=(startPosX+42,startPosY+5),
- font=labelFont,fill=BLACK)
+ text='Dominance Effect', xy=(startPosX+42, startPosY+5),
+ font=labelFont, fill=BLACK)
if self.haplotypeAnalystChecked:
startPosY += stepPosY
startPosX = xLeftOffset
im_drawer.line(
- xy=((startPosX,startPosY),(startPosX+17,startPosY)),
+ xy=((startPosX, startPosY), (startPosX+17, startPosY)),
fill=self.HAPLOTYPE_POSITIVE, width=4)
im_drawer.line(
- xy=((startPosX+18,startPosY),(startPosX+35,startPosY)),
+ xy=((startPosX+18, startPosY), (startPosX+35, startPosY)),
fill=self.HAPLOTYPE_NEGATIVE, width=4)
im_drawer.line(
- xy=((startPosX+36,startPosY),(startPosX+53,startPosY)),
+ xy=((startPosX+36, startPosY), (startPosX+53, startPosY)),
fill=self.HAPLOTYPE_HETEROZYGOUS, width=4)
im_drawer.line(
- xy=((startPosX+54,startPosY),(startPosX+67,startPosY)),
+ xy=((startPosX+54, startPosY), (startPosX+67, startPosY)),
fill=self.HAPLOTYPE_RECOMBINATION, width=4)
im_drawer.text(
text='Haplotypes (Pat, Mat, Het, Unk)',
- xy=(startPosX+76,startPosY+5),font=labelFont,fill=BLACK)
+ xy=(startPosX+76, startPosY+5), font=labelFont, fill=BLACK)
if self.permChecked and self.nperm > 0:
startPosY += stepPosY
startPosX = xLeftOffset
im_drawer.line(
- xy=((startPosX, startPosY),( startPosX + 32, startPosY)),
+ xy=((startPosX, startPosY), ( startPosX + 32, startPosY)),
fill=self.SIGNIFICANT_COLOR, width=self.SIGNIFICANT_WIDTH)
im_drawer.line(
- xy=((startPosX, startPosY + stepPosY),( startPosX + 32, startPosY + stepPosY)),
+ xy=((startPosX, startPosY + stepPosY), ( startPosX + 32, startPosY + stepPosY)),
fill=self.SUGGESTIVE_COLOR, width=self.SUGGESTIVE_WIDTH)
im_drawer.text(
- text='Significant %s = %2.2f' % (self.LRS_LOD,self.significant),
- xy=(xLeftOffset+42,startPosY+TEXT_Y_DISPLACEMENT),font=labelFont,fill=BLACK)
+ text='Significant %s = %2.2f' % (self.LRS_LOD, self.significant),
+ xy=(xLeftOffset+42, startPosY+TEXT_Y_DISPLACEMENT), font=labelFont, fill=BLACK)
im_drawer.text(
text='Suggestive %s = %2.2f' % (self.LRS_LOD, self.suggestive),
- xy=(xLeftOffset+42,startPosY + TEXT_Y_DISPLACEMENT +stepPosY),font=labelFont,
+ xy=(xLeftOffset+42, startPosY + TEXT_Y_DISPLACEMENT +stepPosY), font=labelFont,
fill=BLACK)
- labelFont = ImageFont.truetype(font=VERDANA_FILE,size=12*fontZoom)
+ labelFont = ImageFont.truetype(font=VERDANA_FILE, size=12*fontZoom)
labelColor = BLACK
if self.dataset.type == "Publish" or self.dataset.type == "Geno":
dataset_label = self.dataset.fullname
@@ -1109,22 +1109,22 @@ class DisplayMappingResults(object):
im_drawer.textsize(string2, font=labelFont)[0])
im_drawer.text(
text=identification,
- xy=(canvas.size[0] - xRightOffset-d,20*fontZoom),font=labelFont,
+ xy=(canvas.size[0] - xRightOffset-d, 20*fontZoom), font=labelFont,
fill=labelColor)
else:
d = 4+ max(
im_drawer.textsize(string1, font=labelFont)[0],
im_drawer.textsize(string2, font=labelFont)[0])
im_drawer.text(
- text=string1,xy=(canvas.size[0] - xRightOffset-d,35*fontZoom),
- font=labelFont,fill=labelColor)
+ text=string1, xy=(canvas.size[0] - xRightOffset-d, 35*fontZoom),
+ font=labelFont, fill=labelColor)
im_drawer.text(
- text=string2,xy=(canvas.size[0] - xRightOffset-d,50*fontZoom),
- font=labelFont,fill=labelColor)
+ text=string2, xy=(canvas.size[0] - xRightOffset-d, 50*fontZoom),
+ font=labelFont, fill=labelColor)
if string3 != '':
im_drawer.text(
- text=string3,xy=(canvas.size[0] - xRightOffset-d,65*fontZoom),
- font=labelFont,fill=labelColor)
+ text=string3, xy=(canvas.size[0] - xRightOffset-d, 65*fontZoom),
+ font=labelFont, fill=labelColor)
def drawGeneBand(self, canvas, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
@@ -1345,7 +1345,7 @@ class DisplayMappingResults(object):
labelText = "3'"
im_drawer.text(
text=labelText,
- xy=(utrEndPix+2,geneYLocation+self.EACH_GENE_HEIGHT),
+ xy=(utrEndPix+2, geneYLocation+self.EACH_GENE_HEIGHT),
font=ImageFont.truetype(font=ARIAL_FILE, size=2))
#draw the genes as rectangles
@@ -1357,7 +1357,7 @@ class DisplayMappingResults(object):
COORDS = "%d, %d, %d, %d" %(geneStartPix, geneYLocation, geneEndPix, (geneYLocation + self.EACH_GENE_HEIGHT))
# NL: 06-02-2011 Rob required to display NCBI info in a new window
- gifmap.areas.append(HT.Area(shape='rect',coords=COORDS,href=HREF, title=TITLE,target="_blank"))
+ gifmap.areas.append(HT.Area(shape='rect', coords=COORDS, href=HREF, title=TITLE, target="_blank"))
## BEGIN HaplotypeAnalyst
def drawHaplotypeBand(self, canvas, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
@@ -1490,7 +1490,7 @@ class DisplayMappingResults(object):
counter = counter + 1
if item.name == samplelist[k]:
ind = counter
- maxind=max(ind,maxind)
+ maxind=max(ind, maxind)
# lines
if (oldgeno[k] == -1 and _geno == -1):
@@ -1523,7 +1523,7 @@ class DisplayMappingResults(object):
COORDS = "%d, %d, %d, %d" %(geneStartPix, geneYLocation+ind*self.EACH_GENE_HEIGHT, geneEndPix+1, (geneYLocation + ind*self.EACH_GENE_HEIGHT))
TITLE = "Strain: %s, marker (%s) \n Position %2.3f Mb." % (samplelist[k], _chr[j].name, float(txStart))
HREF = ''
- gifmap.areas.append(HT.Area(shape='rect',coords=COORDS,href=HREF, title=TITLE))
+ gifmap.areas.append(HT.Area(shape='rect', coords=COORDS, href=HREF, title=TITLE))
# if there are no more markers in a chromosome, the plotRight value calculated above will be before the plotWidth
# resulting in some empty space on the right side of the plot area. This draws an "unknown" bar from plotRight to the edge.
@@ -1642,14 +1642,14 @@ class DisplayMappingResults(object):
WEBQTL_HREF = "javascript:rangeView('%s', %f, %f)" % (self.selectedChr - 1, max(0, (calBase-webqtlZoomWidth))/1000000.0, (calBase+webqtlZoomWidth)/1000000.0)
WEBQTL_TITLE = "Click to view this section of the genome in WebQTL"
- gifmap.areas.append(HT.Area(shape='rect',coords=WEBQTL_COORDS,href=WEBQTL_HREF, title=WEBQTL_TITLE))
+ gifmap.areas.append(HT.Area(shape='rect', coords=WEBQTL_COORDS, href=WEBQTL_HREF, title=WEBQTL_TITLE))
im_drawer.rectangle(
xy=((xBrowse1, paddingTop),
(xBrowse2, (paddingTop + self.BAND_HEIGHT))),
outline=self.CLICKABLE_WEBQTL_REGION_COLOR,
fill=self.CLICKABLE_WEBQTL_REGION_COLOR)
im_drawer.line(
- xy=((xBrowse1, paddingTop),( xBrowse1, (paddingTop + self.BAND_HEIGHT))),
+ xy=((xBrowse1, paddingTop), ( xBrowse1, (paddingTop + self.BAND_HEIGHT))),
fill=self.CLICKABLE_WEBQTL_REGION_OUTLINE_COLOR)
if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat":
@@ -1659,14 +1659,14 @@ class DisplayMappingResults(object):
else:
PHENOGEN_HREF = "https://phenogen.org/gene.jsp?speciesCB=Mm&auto=Y&geneTxt=chr%s:%d-%d&genomeVer=mm10" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
PHENOGEN_TITLE = "Click to view this section of the genome in PhenoGen"
- gifmap.areas.append(HT.Area(shape='rect',coords=PHENOGEN_COORDS,href=PHENOGEN_HREF, title=PHENOGEN_TITLE))
+ gifmap.areas.append(HT.Area(shape='rect', coords=PHENOGEN_COORDS, href=PHENOGEN_HREF, title=PHENOGEN_TITLE))
im_drawer.rectangle(
xy=((xBrowse1, phenogenPaddingTop),
(xBrowse2, (phenogenPaddingTop+self.BAND_HEIGHT))),
outline=self.CLICKABLE_PHENOGEN_REGION_COLOR,
fill=self.CLICKABLE_PHENOGEN_REGION_COLOR)
im_drawer.line(
- xy=((xBrowse1, phenogenPaddingTop),( xBrowse1, (phenogenPaddingTop+self.BAND_HEIGHT))),
+ xy=((xBrowse1, phenogenPaddingTop), ( xBrowse1, (phenogenPaddingTop+self.BAND_HEIGHT))),
fill=self.CLICKABLE_PHENOGEN_REGION_OUTLINE_COLOR)
UCSC_COORDS = "%d, %d, %d, %d" %(xBrowse1, ucscPaddingTop, xBrowse2, (ucscPaddingTop+self.BAND_HEIGHT))
@@ -1675,7 +1675,7 @@ class DisplayMappingResults(object):
else:
UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d" % (self._ucscDb, self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
UCSC_TITLE = "Click to view this section of the genome in the UCSC Genome Browser"
- gifmap.areas.append(HT.Area(shape='rect',coords=UCSC_COORDS,href=UCSC_HREF, title=UCSC_TITLE))
+ gifmap.areas.append(HT.Area(shape='rect', coords=UCSC_COORDS, href=UCSC_HREF, title=UCSC_TITLE))
im_drawer.rectangle(
xy=((xBrowse1, ucscPaddingTop),
(xBrowse2, (ucscPaddingTop+self.BAND_HEIGHT))),
@@ -1692,7 +1692,7 @@ class DisplayMappingResults(object):
else:
ENSEMBL_HREF = "http://www.ensembl.org/Rattus_norvegicus/contigview?chr=%s&start=%d&end=%d" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
ENSEMBL_TITLE = "Click to view this section of the genome in the Ensembl Genome Browser"
- gifmap.areas.append(HT.Area(shape='rect',coords=ENSEMBL_COORDS,href=ENSEMBL_HREF, title=ENSEMBL_TITLE))
+ gifmap.areas.append(HT.Area(shape='rect', coords=ENSEMBL_COORDS, href=ENSEMBL_HREF, title=ENSEMBL_TITLE))
im_drawer.rectangle(
xy=((xBrowse1, ensemblPaddingTop),
(xBrowse2, (ensemblPaddingTop+self.BAND_HEIGHT))),
@@ -1789,8 +1789,8 @@ class DisplayMappingResults(object):
continue
Xc = xLeftOffset + plotXScale*(_Mb - startMb)
if counter % NUM_MINOR_TICKS == 0: # Draw a MAJOR mark, not just a minor tick mark
- im_drawer.line(xy=((Xc,yZero),
- (Xc,yZero+xMajorTickHeight)),
+ im_drawer.line(xy=((Xc, yZero),
+ (Xc, yZero+xMajorTickHeight)),
fill=xAxisTickMarkColor,
width=X_MAJOR_TICK_THICKNESS) # Draw the MAJOR tick mark
labelStr = str(formatStr % _Mb) # What Mbase location to put on the label
@@ -1800,8 +1800,8 @@ class DisplayMappingResults(object):
text=labelStr, font=MBLabelFont,
fill=xAxisLabelColor)
else:
- im_drawer.line(xy=((Xc,yZero),
- (Xc,yZero+xMinorTickHeight)),
+ im_drawer.line(xy=((Xc, yZero),
+ (Xc, yZero+xMinorTickHeight)),
fill=xAxisTickMarkColor,
width=X_MINOR_TICK_THICKNESS) # Draw the MINOR tick mark
@@ -1834,7 +1834,7 @@ class DisplayMappingResults(object):
text="Megabases",
xy=(
xLeftOffset+(plotWidth-im_drawer.textsize(
- "Megabases",font=megabaseLabelFont)[0])/2,
+ "Megabases", font=megabaseLabelFont)[0])/2,
strYLoc+MBLabelFont.font.height+10*(zoom%2)),
font=megabaseLabelFont, fill=BLACK)
pass
@@ -1889,7 +1889,7 @@ class DisplayMappingResults(object):
for j, ChrInfo in enumerate(ChrAInfo):
preLpos = -1
for i, item in enumerate(ChrInfo):
- Lname,Lpos = item
+ Lname, Lpos = item
if Lpos != preLpos:
offsetA += stepA
differ = 1
@@ -1903,17 +1903,17 @@ class DisplayMappingResults(object):
Zorder = 0
if differ:
im_drawer.line(
- xy=((startPosX+Lpos,yZero),(xLeftOffset+offsetA,\
+ xy=((startPosX+Lpos, yZero), (xLeftOffset+offsetA,\
yZero+25)),
fill=lineColor)
im_drawer.line(
- xy=((xLeftOffset+offsetA,yZero+25),(xLeftOffset+offsetA,\
+ xy=((xLeftOffset+offsetA, yZero+25), (xLeftOffset+offsetA,\
yZero+40+Zorder*(LRectWidth+3))),
fill=lineColor)
rectColor = ORANGE
else:
im_drawer.line(
- xy=((xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3)-3),(\
+ xy=((xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3)-3), (\
xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3))),
fill=lineColor)
rectColor = DEEPPINK
@@ -1921,9 +1921,9 @@ class DisplayMappingResults(object):
xy=((xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3)),
(xLeftOffset+offsetA-LRectHeight,
yZero+40+Zorder*(LRectWidth+3)+LRectWidth)),
- outline=rectColor,fill=rectColor,width = 0)
+ outline=rectColor, fill=rectColor, width = 0)
COORDS="%d,%d,%d,%d"%(xLeftOffset+offsetA-LRectHeight, yZero+40+Zorder*(LRectWidth+3),\
- xLeftOffset+offsetA,yZero+40+Zorder*(LRectWidth+3)+LRectWidth)
+ xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3)+LRectWidth)
HREF="/show_trait?trait_id=%s&dataset=%s" % (Lname, self.dataset.group.name+"Geno")
#HREF="javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm,fd.RISet+"Geno", Lname)
Areas=HT.Area(shape='rect', coords=COORDS, href=HREF, target="_blank", title="Locus : " + Lname)
@@ -1931,7 +1931,7 @@ class DisplayMappingResults(object):
##piddle bug
if j == 0:
im_drawer.line(
- xy=((startPosX,yZero),(startPosX,yZero+40)),
+ xy=((startPosX, yZero), (startPosX, yZero+40)),
fill=lineColor)
startPosX += (self.ChrLengthDistList[j]+self.GraphInterval)*plotXScale
@@ -1943,7 +1943,7 @@ class DisplayMappingResults(object):
strYLoc + MBLabelFont.font.height+ 10*(zoom%2)),
font=centimorganLabelFont, fill=BLACK)
- im_drawer.line(xy=((xLeftOffset,yZero), (xLeftOffset+plotWidth,yZero)),
+ im_drawer.line(xy=((xLeftOffset, yZero), (xLeftOffset+plotWidth, yZero)),
fill=BLACK, width=X_AXIS_THICKNESS) # Draw the X axis itself
@@ -2079,7 +2079,7 @@ class DisplayMappingResults(object):
LRS_LOD_Max = 0.000001
yTopOffset + 30*(zoom - 1)
yLRS = yZero - (item/LRS_LOD_Max) * LRSHeightThresh
- im_drawer.line(xy=((xLeftOffset,yLRS), (xLeftOffset-4,yLRS)),
+ im_drawer.line(xy=((xLeftOffset, yLRS), (xLeftOffset-4, yLRS)),
fill=self.LRS_COLOR, width=1*zoom)
if all_int:
scaleStr = "%d" % item
@@ -2127,8 +2127,8 @@ class DisplayMappingResults(object):
else:
sugg_title = "Suggestive LOD = %0.2f" % (self.suggestive/4.61)
sig_title = "Significant LOD = %0.2f" % (self.significant/4.61)
- Areas1 = HT.Area(shape='rect',coords=sugg_coords,title=sugg_title)
- Areas2 = HT.Area(shape='rect',coords=sig_coords,title=sig_title)
+ Areas1 = HT.Area(shape='rect', coords=sugg_coords, title=sugg_title)
+ Areas2 = HT.Area(shape='rect', coords=sig_coords, title=sig_title)
gifmap.areas.append(Areas1)
gifmap.areas.append(Areas2)
@@ -2316,7 +2316,7 @@ class DisplayMappingResults(object):
im_drawer.text(
text="5",
xy=(
- Xc-im_drawer.textsize("5",font=symbolFont)[0]/2+1,
+ Xc-im_drawer.textsize("5", font=symbolFont)[0]/2+1,
Yc-4),
fill=point_color, font=symbolFont)
else:
@@ -2383,8 +2383,8 @@ class DisplayMappingResults(object):
)
else:
im_drawer.line(
- xy=((Xc0,yZero-(Yc0-yZero)),
- (Xc,yZero-(Yc-yZero))),
+ xy=((Xc0, yZero-(Yc0-yZero)),
+ (Xc, yZero-(Yc-yZero))),
fill=minusColor, width=lineWidth
#, clipX=(xLeftOffset, xLeftOffset + plotWidth)
)
@@ -2471,8 +2471,8 @@ class DisplayMappingResults(object):
###draw additive scale
if not self.multipleInterval and self.additiveChecked:
- additiveScaleFont=ImageFont.truetype(font=VERDANA_FILE,size=16*zoom)
- additiveScale = Plot.detScaleOld(0,additiveMax)
+ additiveScaleFont=ImageFont.truetype(font=VERDANA_FILE, size=16*zoom)
+ additiveScale = Plot.detScaleOld(0, additiveMax)
additiveStep = (additiveScale[1]-additiveScale[0])/additiveScale[2]
additiveAxisList = Plot.frange(0, additiveScale[1], additiveStep)
addPlotScale = AdditiveHeightThresh/additiveMax
@@ -2482,18 +2482,18 @@ class DisplayMappingResults(object):
for item in additiveAxisList:
additiveY = yZero - item*addPlotScale
im_drawer.line(
- xy=((xLeftOffset + plotWidth,additiveY),
- (xLeftOffset+4+ plotWidth,additiveY)),
+ xy=((xLeftOffset + plotWidth, additiveY),
+ (xLeftOffset+4+ plotWidth, additiveY)),
fill=self.ADDITIVE_COLOR_POSITIVE, width=1*zoom)
scaleStr = "%2.3f" % item
im_drawer.text(
text=scaleStr,
- xy=(xLeftOffset + plotWidth +6,additiveY+TEXT_Y_DISPLACEMENT),
- font=additiveScaleFont,fill=self.ADDITIVE_COLOR_POSITIVE)
+ xy=(xLeftOffset + plotWidth +6, additiveY+TEXT_Y_DISPLACEMENT),
+ font=additiveScaleFont, fill=self.ADDITIVE_COLOR_POSITIVE)
im_drawer.line(
- xy=((xLeftOffset+plotWidth,additiveY),
- (xLeftOffset+plotWidth,yZero)),
+ xy=((xLeftOffset+plotWidth, additiveY),
+ (xLeftOffset+plotWidth, yZero)),
fill=self.ADDITIVE_COLOR_POSITIVE, width=1*zoom)
im_drawer.line(
@@ -2553,7 +2553,7 @@ class DisplayMappingResults(object):
chrFontZoom = 2
else:
chrFontZoom = 1
- chrLabelFont=ImageFont.truetype(font=VERDANA_FILE,size=24*chrFontZoom)
+ chrLabelFont=ImageFont.truetype(font=VERDANA_FILE, size=24*chrFontZoom)
for i, _chr in enumerate(self.genotype):
if (i % 2 == 0):
@@ -2575,10 +2575,10 @@ class DisplayMappingResults(object):
TEXT_Y_DISPLACEMENT = 0
im_drawer.text(xy=(chrStartPix, yTopOffset + TEXT_Y_DISPLACEMENT),
text=_chr.name, font=chrLabelFont, fill=BLACK)
- COORDS = "%d,%d,%d,%d" %(chrStartPix, yTopOffset, chrEndPix,yTopOffset +20)
+ COORDS = "%d,%d,%d,%d" %(chrStartPix, yTopOffset, chrEndPix, yTopOffset +20)
#add by NL 09-03-2010
- HREF = "javascript:chrView(%d,%s);" % (i,self.ChrLengthMbList)
+ HREF = "javascript:chrView(%d,%s);" % (i, self.ChrLengthMbList)
#HREF = "javascript:changeView(%d,%s);" % (i,self.ChrLengthMbList)
Areas = HT.Area(shape='rect', coords=COORDS, href=HREF)
gifmap.areas.append(Areas)
@@ -2720,7 +2720,7 @@ class DisplayMappingResults(object):
else:
chr_as_int = int(theGO["Chromosome"]) - 1
if refGene:
- literatureCorrelationString = str(self.getLiteratureCorrelation(self.cursor,refGene,theGO['GeneID']) or "N/A")
+ literatureCorrelationString = str(self.getLiteratureCorrelation(self.cursor, refGene, theGO['GeneID']) or "N/A")
this_row = [selectCheck.__str__(),
str(tableIterationsCnt),
@@ -2820,8 +2820,8 @@ class DisplayMappingResults(object):
lCorr = None
try:
query = 'SELECT Value FROM LCorrRamin3 WHERE GeneId1 = %s and GeneId2 = %s'
- for x,y in [(geneId1,geneId2),(geneId2,geneId1)]:
- cursor.execute(query,(x,y))
+ for x, y in [(geneId1, geneId2), (geneId2, geneId1)]:
+ cursor.execute(query, (x, y))
lCorr = cursor.fetchone()
if lCorr:
lCorr = lCorr[0]
diff --git a/wqflask/wqflask/marker_regression/plink_mapping.py b/wqflask/wqflask/marker_regression/plink_mapping.py
index d4ee6fe6..2f282adc 100644
--- a/wqflask/wqflask/marker_regression/plink_mapping.py
+++ b/wqflask/wqflask/marker_regression/plink_mapping.py
@@ -54,7 +54,7 @@ def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename = ''):
for i, sample in enumerate(ped_sample_list):
try:
value = vals[i]
- value = str(value).replace('value=','')
+ value = str(value).replace('value=', '')
value = value.strip()
except:
value = -9999
@@ -78,7 +78,7 @@ def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename = ''):
# get strain name from ped file in order
def get_samples_from_ped_file(dataset):
- ped_file= open("{}{}.ped".format(flat_files('mapping'), dataset.group.name),"r")
+ ped_file= open("{}{}.ped".format(flat_files('mapping'), dataset.group.name), "r")
line = ped_file.readline()
sample_list=[]
@@ -155,7 +155,7 @@ def parse_plink_output(output_filename, species):
# output: lineList list
#######################################################
def build_line_list(line=None):
- line_list = string.split(string.strip(line),' ')# irregular number of whitespaces between columns
+ line_list = string.split(string.strip(line), ' ')# irregular number of whitespaces between columns
line_list = [item for item in line_list if item !='']
line_list = list(map(string.strip, line_list))
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 145dbc77..1e6dff57 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -707,7 +707,7 @@ def get_perm_strata(this_trait, sample_list, categorical_vars, used_samples):
perm_strata_strings.append(combined_string)
- d = dict([(y,x+1) for x,y in enumerate(sorted(set(perm_strata_strings)))])
+ d = dict([(y, x+1) for x, y in enumerate(sorted(set(perm_strata_strings)))])
list_to_numbers = [d[x] for x in perm_strata_strings]
perm_strata = list_to_numbers
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index 5b3946e3..c07a7670 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -53,7 +53,7 @@ views.py).
search = self.search_terms
self.original_search_string = self.search_terms
# check for dodgy search terms
- rx = re.compile(r'.*\W(href|http|sql|select|update)\W.*',re.IGNORECASE)
+ rx = re.compile(r'.*\W(href|http|sql|select|update)\W.*', re.IGNORECASE)
if rx.match(search):
logger.info("Regex failed search")
self.search_term_exists = False
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index 21ba7f63..f17e825e 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -57,7 +57,7 @@ class SampleList(object):
sample = webqtlCaseData.webqtlCaseData(name=sample_name)
sample.extra_info = {}
- if self.dataset.group.name == 'AXBXA' and sample_name in ('AXB18/19/20','AXB13/14','BXA8/17'):
+ if self.dataset.group.name == 'AXBXA' and sample_name in ('AXB18/19/20', 'AXB13/14', 'BXA8/17'):
sample.extra_info['url'] = "/mouseCross.html#AXB/BXA"
sample.extra_info['css_class'] = "fs12"
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index a871e91a..232cb8da 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -867,7 +867,7 @@ def forgot_password_submit():
email_address = params['email_address']
next_page = None
if email_address != "":
- logger.debug("Wants to send password E-mail to ",email_address)
+ logger.debug("Wants to send password E-mail to ", email_address)
user_details = get_user_by_unique_column("email_address", email_address)
if user_details:
ForgotPasswordEmail(user_details["email_address"])
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 394a9e28..92c20fc7 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -55,7 +55,7 @@ from wqflask.ctl import ctl_analysis
from wqflask.snp_browser import snp_browser
from utility import temp_data
-from utility.tools import SQL_URI,TEMPDIR,USE_REDIS,USE_GN_SERVER,GN_SERVER_URL,GN_VERSION,JS_TWITTER_POST_FETCHER_PATH,JS_GUIX_PATH, CSS_PATH
+from utility.tools import SQL_URI, TEMPDIR, USE_REDIS, USE_GN_SERVER, GN_SERVER_URL, GN_VERSION, JS_TWITTER_POST_FETCHER_PATH, JS_GUIX_PATH, CSS_PATH
from utility.helper_functions import get_species_groups
from utility.authentication_tools import check_resource_availability
from utility.redis_tools import get_redis_conn
@@ -133,10 +133,10 @@ def handle_bad_request(e):
list = [fn for fn in os.listdir("./wqflask/static/gif/error") if fn.endswith(".gif") ]
animation = random.choice(list)
- resp = make_response(render_template("error.html",message=err_msg,stack=formatted_lines,error_image=animation,version=GN_VERSION))
+ resp = make_response(render_template("error.html", message=err_msg, stack=formatted_lines, error_image=animation, version=GN_VERSION))
# logger.error("Set cookie %s with %s" % (err_msg, animation))
- resp.set_cookie(err_msg[:32],animation)
+ resp.set_cookie(err_msg[:32], animation)
return resp
@app.route("/authentication_needed")
@@ -257,7 +257,7 @@ def docedit():
@app.route('/generated/<filename>')
def generated_file(filename):
logger.info(request.url)
- return send_from_directory(GENERATED_IMAGE_DIR,filename)
+ return send_from_directory(GENERATED_IMAGE_DIR, filename)
@app.route("/help")
def help():