class Axis(object):
def __init__(self, scale, variant, allele):
self.scale = scale
self.allele = allele
self.variant = variant
self.chromPartsCollection = variant.chromParts(allele)
self.height = 75
def baseHeight(self):
return 75
def render(self, scaleFactor=1.0, spacing=1.0, height=None, thickerLines=False):
self.height = height
if height == None:
self.height = 75 * scaleFactor
self.svg = SVG(self.scale.pixelWidth, self.height, yrelto="top", headerExtras="""preserveAspectRatio="none" """)
# dividers! (multi-part only)
if len(self.chromPartsCollection) > 1:
for part in list(self.chromPartsCollection)[1:]:
divWidth = self.scale.relpixels(self.scale.dividerSize)
x = self.scale.partsToStartPixels[part.id] - divWidth
self.svg.rect(x, 0, divWidth, self.height, fill="#B2B2B2")
self.svg.line(x, 0, x, self.height, stroke="black", **{"stroke-width":1*scaleFactor})
self.svg.line(x+divWidth, 0, x+divWidth, self.height, stroke="black", **{"stroke-width":1*scaleFactor})
for i, part in enumerate(self.chromPartsCollection):
if i == 0:
x = self.scale.topixels(self.scale.partsToLengths[part.id], part.id) - 15
anchor = "end"
else:
x = self.scale.partsToStartPixels[part.id] + 15
anchor = "start"
self.svg.text(x, 18*scaleFactor, part.id, anchor=anchor, size=18*scaleFactor)
# tick marks and coordinates
for regionID in self.scale.partsToStartPixels:
for tick in self.getTicks(regionID):
x = self.scale.topixels(tick, regionID)
self.svg.rect(x, 35*scaleFactor, 1*scaleFactor, 15*scaleFactor, fill="black")
label = tick
if tick > 1e6:
label = "{:.1f}MB".format(tick/1e6)
elif tick > 1e3:
label = "{:.1f}KB".format(tick/1e3)
if x < 50:
x = 50
elif x > self.scale.pixelWidth - 50:
x = self.scale.pixelWidth - 50
extras = {}
if thickerLines:
extras["font-weight"] = "bold"
self.svg.text(x, self.height-4*scaleFactor, label, size=18*scaleFactor, **extras)
# segment arrows
for part in self.chromPartsCollection:
curOffset = self.scale.partsToStartPixels[part.id]
for segment in part.segments:
start = curOffset
end = self.scale.relpixels(len(segment)) + curOffset
curOffset = end
arrowDirection = "right"
if segment.strand == "-":
start, end = end, start
arrowDirection = "left"
y = 35*scaleFactor
self.svg.line(start, y, end, y, stroke=segment.color(), **{"stroke-width":8*scaleFactor})
self.svg.lineWithInternalArrows(start, y, end, y, stroke=segment.color(), direction=arrowDirection,
arrowKwdArgs={"class":"scaleArrow"}, **{"stroke-width":3*scaleFactor})
# breakpoints
previousPosition = None
for part in self.chromPartsCollection:
for vline in self.scale.getBreakpointPositions(part.id):
thickness = 1*scaleFactor
if thickerLines:
thickness *= 2
x = self.scale.topixels(vline, part.id)
self.svg.line(x, 20*scaleFactor, x, 55*scaleFactor,
stroke="black", **{"stroke-width":thickness})
if previousPosition is None or x-previousPosition > 250*scaleFactor:
self.svg.text(x-(scaleFactor/2.0), 18*scaleFactor, "breakpoint", size=18*scaleFactor, fill="black")
previousPosition = x
return str(self.svg)
def getTicks(self, regionID):
ticks = []
start = 0
width = self.scale.partsToLengths[regionID]
end = start + width
res = (10 ** round(math.log10(end - start))) / 10.0
if width / res > 15:
res *= 2.5
elif width / res < 5:
res /= 2.0
roundStart = start - (start%res)
for i in range(int(roundStart), end, int(res)):
ticks.append(i)
return ticks
class Axis(object):
def __init__(self, scale, variant, allele):
self.scale = scale
self.allele = allele
self.variant = variant
self.chromPartsCollection = variant.chromParts(allele)
self.height = 75
def baseHeight(self):
return 75
def render(self, scaleFactor=1.0, spacing=1.0, height=None, thickerLines=False):
self.height = height
if height == None:
self.height = 75 * scaleFactor
self.svg = SVG(self.scale.pixelWidth, self.height, yrelto="top", headerExtras="""preserveAspectRatio="none" """)
# dividers! (multi-part only)
if len(self.chromPartsCollection) > 1:
for part in list(self.chromPartsCollection)[1:]:
divWidth = self.scale.relpixels(self.scale.dividerSize)
x = self.scale.partsToStartPixels[part.id] - divWidth
self.svg.rect(x, 0, divWidth, self.height, fill="#B2B2B2")
self.svg.line(x, 0, x, self.height, stroke="black", **{"stroke-width":1*scaleFactor})
self.svg.line(x+divWidth, 0, x+divWidth, self.height, stroke="black", **{"stroke-width":1*scaleFactor})
for i, part in enumerate(self.chromPartsCollection):
if i == 0:
x = self.scale.topixels(self.scale.partsToLengths[part.id], part.id) - 15
anchor = "end"
else:
x = self.scale.partsToStartPixels[part.id] + 15
anchor = "start"
self.svg.text(x, 18*scaleFactor, part.id, anchor=anchor, size=18*scaleFactor)
# tick marks and coordinates
for regionID in self.scale.partsToStartPixels:
for tick in self.getTicks(regionID):
x = self.scale.topixels(tick, regionID)
self.svg.rect(x, 35*scaleFactor, 1*scaleFactor, 15*scaleFactor, fill="black")
label = tick
if tick > 1e6:
label = "{:.1f}MB".format(tick/1e6)
elif tick > 1e3:
label = "{:.1f}KB".format(tick/1e3)
if x < 50:
x = 50
elif x > self.scale.pixelWidth - 50:
x = self.scale.pixelWidth - 50
extras = {}
if thickerLines:
extras["font-weight"] = "bold"
self.svg.text(x, self.height-4*scaleFactor, label, size=18*scaleFactor, **extras)
# segment arrows
for part in self.chromPartsCollection:
curOffset = self.scale.partsToStartPixels[part.id]
for segment in part.segments:
start = curOffset
end = self.scale.relpixels(len(segment)) + curOffset
curOffset = end
arrowDirection = "right"
if segment.strand == "-":
start, end = end, start
arrowDirection = "left"
y = 35*scaleFactor
self.svg.line(start, y, end, y, stroke=segment.color(), **{"stroke-width":8*scaleFactor})
self.svg.lineWithInternalArrows(start, y, end, y, stroke=segment.color(), direction=arrowDirection,
arrowKwdArgs={"class":"scaleArrow"}, **{"stroke-width":3*scaleFactor})
# breakpoints
previousPosition = None
for part in self.chromPartsCollection:
for vline in self.scale.getBreakpointPositions(part.id):
thickness = 1*scaleFactor
if thickerLines:
thickness *= 2
x = self.scale.topixels(vline, part.id)
self.svg.line(x, 20*scaleFactor, x, 55*scaleFactor,
stroke="black", **{"stroke-width":thickness})
if previousPosition is None or x-previousPosition > 250*scaleFactor:
self.svg.text(x-(scaleFactor/2.0), 18*scaleFactor, "breakpoint", size=18*scaleFactor, fill="black")
previousPosition = x
return str(self.svg)
def getTicks(self, regionID):
ticks = []
start = 0
width = self.scale.partsToLengths[regionID]
end = start + width
res = (10 ** round(math.log10(end - start))) / 10.0
if width / res > 15:
res *= 2.5
elif width / res < 5:
res /= 2.0
roundStart = start - (start%res)
for i in range(int(roundStart), end, int(res)):
ticks.append(i)
return ticks
class Track(object):
def __init__(self, chromPartsCollection, alignmentSets, height, width, variant, allele, thickerLines, colorCigar):
self.chromPartsCollection = chromPartsCollection
self.height = height
self.width = width
self.scale = Scale(chromPartsCollection, width)
self.rowHeight = 5
self.rowMargin = 1
self.readRenderer = ReadRenderer(self.rowHeight, self.scale, self.chromPartsCollection, thickerLines, colorCigar)
self.alignmentSets = alignmentSets
self.svg = None
self.rendered = None
self.variant = variant
self.allele = allele
self.rows = []
self._axis = None
self.xmin = None
self.xmax = None
self.thickerLines = thickerLines
def findRow(self, start, end, regionID):
for currow in range(len(self.rows)):
if self.rows[currow] is None or (start - self.rows[currow]) >= 2:
self.rows[currow] = end
break
else:
self.rows.append(end)
currow = len(self.rows)-1
return currow
def getAlignments(self):
# check which reads are overlapping (self.gstart, self.gend)
# sorting by name makes the layout process deterministic
regionIDsToPositions = dict((part.id, i) for i, part in enumerate(self.chromPartsCollection))
def sortKey(alnSet):
return (regionIDsToPositions[alnSet.getAlignments()[0].regionID],
alnSet.start, alnSet.end, alnSet.name())
return sorted(self.alignmentSets, key=sortKey)
def dolayout(self):
self.rows = [None]#*numRows
self.xmin = 1e100
self.xmax = 0
for alignmentSet in self.getAlignments():
# if len(alignmentSet.getAlignments()) < 2:
# continue
regionIDs = set([x.regionID for x in alignmentSet.getAlignments()])
assert self.allele=="amb" or len(regionIDs)==1, alignmentSet.getAlignments()
regionID = regionIDs.pop()
start = self.scale.topixels(alignmentSet.start, regionID)
end = self.scale.topixels(alignmentSet.end, regionID)
currow = self.findRow(start, end, regionID)
yoffset = (self.rowHeight+self.rowMargin) * currow
alignmentSet.yoffset = yoffset
self.xmin = min(self.xmin, self.scale.topixels(alignmentSet.start, regionID))
self.xmax = max(self.xmax, self.scale.topixels(alignmentSet.end, regionID))
self.height = (self.rowHeight+self.rowMargin) * len(self.rows)
def render(self):
if len(self.getAlignments()) == 0:
xmiddle = self.scale.pixelWidth / 2.0
self.height = xmiddle/20.0
self.svg = SVG(self.width, self.height)
self.svg.text(xmiddle, self.height*0.05, "No reads found", size=self.height*0.9, fill="#999999")
self.rendered = self.svg.asString()
return self.rendered
self.dolayout()
self.svg = SVG(self.width, self.height)
self.readRenderer.svg = self.svg
alnSets = self.getAlignments()
flankingAlignments = [alnSet for alnSet in alnSets if alnSet.parentCollection.why == "flanking"]
nonFlankingAlignments = [alnSet for alnSet in alnSets if alnSet.parentCollection.why != "flanking"]
for alignmentSet in flankingAlignments+nonFlankingAlignments:
self.readRenderer.render(alignmentSet)
lineWidth = 1 if not self.thickerLines else 3
lineWidth = lineWidth * ((self.xmax-self.xmin)/1200.0)
for part in self.chromPartsCollection:
for vline in self.scale.getBreakpointPositions(part.id):
x = self.scale.topixels(vline, part.id)
y1 = -20
y2 = self.height+20
self.svg.line(x, y1, x, y2, stroke="black", **{"stroke-width":lineWidth})
# dividers!
for part in list(self.chromPartsCollection)[1:]:
divWidth = self.scale.relpixels(self.scale.dividerSize)
x = self.scale.partsToStartPixels[part.id] - divWidth
self.svg.rect(x, self.height+40, divWidth, self.height+40, fill="#B2B2B2")
self.svg.line(x, 0, x, self.height+40, stroke="black", **{"stroke-width":4})
self.svg.line(x+divWidth, 0, x+divWidth, self.height+40, stroke="black", **{"stroke-width":4})
self.svg.rect(0, self.svg.height+20, self.scale.pixelWidth,
self.height+40, opacity=0.0, zindex=0)
self.rendered = str(self.svg)
return self.rendered
class Track(object):
def __init__(self, chromPartsCollection, alignmentSets, height, width, variant, allele, thickerLines, colorCigar):
self.chromPartsCollection = chromPartsCollection
self.height = height
self.width = width
self.scale = Scale(chromPartsCollection, width)
self.rowHeight = 5
self.rowMargin = 1
self.readRenderer = ReadRenderer(self.rowHeight, self.scale, self.chromPartsCollection, thickerLines, colorCigar)
self.alignmentSets = alignmentSets
self.svg = None
self.rendered = None
self.variant = variant
self.allele = allele
self.rows = []
self._axis = None
self.xmin = None
self.xmax = None
self.thickerLines = thickerLines
def findRow(self, start, end, regionID):
for currow in range(len(self.rows)):
if self.rows[currow] is None or (start - self.rows[currow]) >= 2:
self.rows[currow] = end
break
else:
self.rows.append(end)
currow = len(self.rows)-1
return currow
def getAlignments(self):
# check which reads are overlapping (self.gstart, self.gend)
# sorting by name makes the layout process deterministic
regionIDsToPositions = dict((part.id, i) for i, part in enumerate(self.chromPartsCollection))
def sortKey(alnSet):
return (regionIDsToPositions[alnSet.getAlignments()[0].regionID],
alnSet.start, alnSet.end, alnSet.name())
return sorted(self.alignmentSets, key=sortKey)
def dolayout(self):
self.rows = [None]#*numRows
self.xmin = 1e100
self.xmax = 0
for alignmentSet in self.getAlignments():
# if len(alignmentSet.getAlignments()) < 2:
# continue
regionIDs = set([x.regionID for x in alignmentSet.getAlignments()])
assert self.allele=="amb" or len(regionIDs)==1, alignmentSet.getAlignments()
regionID = regionIDs.pop()
start = self.scale.topixels(alignmentSet.start, regionID)
end = self.scale.topixels(alignmentSet.end, regionID)
currow = self.findRow(start, end, regionID)
yoffset = (self.rowHeight+self.rowMargin) * currow
alignmentSet.yoffset = yoffset
self.xmin = min(self.xmin, self.scale.topixels(alignmentSet.start, regionID))
self.xmax = max(self.xmax, self.scale.topixels(alignmentSet.end, regionID))
self.height = (self.rowHeight+self.rowMargin) * len(self.rows)
def render(self):
if len(self.getAlignments()) == 0:
xmiddle = self.scale.pixelWidth / 2.0
self.height = xmiddle/20.0
self.svg = SVG(self.width, self.height)
self.svg.text(xmiddle, self.height*0.05, "No reads found", size=self.height*0.9, fill="#999999")
self.rendered = self.svg.asString()
return self.rendered
self.dolayout()
self.svg = SVG(self.width, self.height)
self.readRenderer.svg = self.svg
alnSets = self.getAlignments()
flankingAlignments = [alnSet for alnSet in alnSets if alnSet.parentCollection.why == "flanking"]
nonFlankingAlignments = [alnSet for alnSet in alnSets if alnSet.parentCollection.why != "flanking"]
for alignmentSet in flankingAlignments+nonFlankingAlignments:
self.readRenderer.render(alignmentSet)
lineWidth = 1 if not self.thickerLines else 3
lineWidth = lineWidth * ((self.xmax-self.xmin)/1200.0)
for part in self.chromPartsCollection:
for vline in self.scale.getBreakpointPositions(part.id):
x = self.scale.topixels(vline, part.id)
y1 = -20
y2 = self.height+20
self.svg.line(x, y1, x, y2, stroke="black", **{"stroke-width":lineWidth})
# dividers!
for part in list(self.chromPartsCollection)[1:]:
divWidth = self.scale.relpixels(self.scale.dividerSize)
x = self.scale.partsToStartPixels[part.id] - divWidth
self.svg.rect(x, self.height+40, divWidth, self.height+40, fill="#B2B2B2")
self.svg.line(x, 0, x, self.height+40, stroke="black", **{"stroke-width":4})
self.svg.line(x+divWidth, 0, x+divWidth, self.height+40, stroke="black", **{"stroke-width":4})
self.svg.rect(0, self.svg.height+20, self.scale.pixelWidth,
self.height+40, opacity=0.0, zindex=0)
self.rendered = str(self.svg)
return self.rendered
