def dolayout(self, scaleFactor, spacing):
# coordinates are in pixels not base pairs
self.rows = [None]
self._annos = []
for part in self.chromPartsCollection:
segmentStart = self.scale.partsToStartPixels[part.id]
for segment in variants.mergedSegments(part.segments):
curWidth = len(segment)
curAnnos = self.annotationSet.getAnnotations(segment.chrom,
segment.start,
segment.end,
clip=True)
if segment.strand == "-":
curAnnos = sorted(curAnnos,
key=lambda x: x.end,
reverse=True)
for anno in curAnnos:
start = max(anno.start, segment.start)
end = min(anno.end, segment.end)
start = self._topixels(start, segment, segmentStart)
end = self._topixels(end, segment, segmentStart)
if end < start:
start, end = end, start
textLength = len(
anno.label
) * self.rowheight / 1.0 * scaleFactor * spacing
rowNum = self.findRow(start, end + textLength)
anno.coords = {}
anno.coords["row"] = rowNum
anno.coords["start"] = start
anno.coords["end"] = end
anno.coords[
"strand"] = anno.strand if segment.strand == "+" else utilities.switchStrand(
anno.strand)
anno.coords["segment"] = segment
anno.coords["segmentStart"] = segmentStart
self._annos.append(anno)
segmentStart += self.scale.relpixels(curWidth)
def dolayout(self, scaleFactor, spacing):
# coordinates are in pixels not base pairs
self.rows = [None]
self._annos = []
for part in self.chromPartsCollection:
segmentStart = self.scale.partsToStartPixels[part.id]
for segment in variants.mergedSegments(part.segments):
curWidth = len(segment)
curAnnos = self.annotationSet.getAnnotations(segment.chrom, segment.start, segment.end, clip=True)
if segment.strand == "-":
curAnnos = sorted(curAnnos, key=lambda x:x.end, reverse=True)
for anno in curAnnos:
start = max(anno.start, segment.start)
end = min(anno.end, segment.end)
start = self._topixels(start, segment, segmentStart)
end = self._topixels(end, segment, segmentStart)
if end < start:
start, end = end, start
textLength = len(anno.name)*self.rowheight/1.0*scaleFactor*spacing
rowNum = self.findRow(start, end+textLength)
anno.coords = {}
anno.coords["row"] = rowNum
anno.coords["start"] = start
anno.coords["end"] = end
anno.coords["strand"] = anno.strand if segment.strand=="+" else utilities.switchStrand(anno.strand)
anno.coords["segment"] = segment
anno.coords["segmentStart"] = segmentStart
self._annos.append(anno)
segmentStart += self.scale.relpixels(curWidth)
def __str__(self):
return "(" + self._chr + ":" + str(self.start()) + "-" + str(
self.end()) + self._strand + ")"
if __name__ == '__main__':
# loci = [Locus("chr1", 10, 20, "+"),
# Locus("chr1", 18, 22, "+"),
# Locus("chr1", 22, 25, "+"),
# Locus("chr1", 27, 30, "+"),
# Locus("chr1", 28, 31, "+"),
# Locus("chr1", 35, 40, "+"),
# Locus("chr1", 42, 45, "+"),
# Locus("chr1", 43, 44, "+")]
# print unionLoci(loci)
from svviz.variants import Segment, mergedSegments
segments = [
Segment("chr100", 1, 3, "+", 0),
Segment("chr100", 5, 9, "+", 1),
Segment("chr100", 11, 15, "+", 2),
Segment("chr100", 17, 19, "+", 3),
Segment("chr100", 21, 31, "+", 4),
Segment("chr100", 33, 34, "+", 5)
]
print segments
print mergedSegments(segments)
def __str__(self):
return "(" + self._chr + ":" + str(self.start()) + "-" + str(
self.end()) + self._strand + ")"
if __name__ == '__main__':
# loci = [Locus("chr1", 10, 20, "+"),
# Locus("chr1", 18, 22, "+"),
# Locus("chr1", 22, 25, "+"),
# Locus("chr1", 27, 30, "+"),
# Locus("chr1", 28, 31, "+"),
# Locus("chr1", 35, 40, "+"),
# Locus("chr1", 42, 45, "+"),
# Locus("chr1", 43, 44, "+")]
# print unionLoci(loci)
from svviz.variants import Segment, mergedSegments
segments = [
Segment("chr100", 1, 3, "+", 0),
Segment("chr100", 5, 9, "+", 1),
Segment("chr100", 11, 15, "+", 2),
Segment("chr100", 17, 19, "+", 3),
Segment("chr100", 21, 31, "+", 4),
Segment("chr100", 33, 34, "+", 5)
]
print(segments)
print(mergedSegments(segments))
def __repr__(self):
return "Locus%s"%str(self)
def __str__(self):
return "(" + self._chr +":" + str(self.start()) + "-" + str(self.end()) + self._strand + ")"
if __name__ == '__main__':
# loci = [Locus("chr1", 10, 20, "+"),
# Locus("chr1", 18, 22, "+"),
# Locus("chr1", 22, 25, "+"),
# Locus("chr1", 27, 30, "+"),
# Locus("chr1", 28, 31, "+"),
# Locus("chr1", 35, 40, "+"),
# Locus("chr1", 42, 45, "+"),
# Locus("chr1", 43, 44, "+")]
# print unionLoci(loci)
from svviz.variants import Segment, mergedSegments
segments = [Segment("chr100", 1,3, "+", 0),
Segment("chr100", 5, 9, "+", 1),
Segment("chr100", 11, 15, "+", 2),
Segment("chr100", 17, 19, "+", 3),
Segment("chr100", 21, 31, "+", 4),
Segment("chr100", 33, 34, "+", 5)]
print(segments)
print(mergedSegments(segments))
def __repr__(self):
return "Locus%s"%str(self)
def __str__(self):
return "(" + self._chr +":" + str(self.start()) + "-" + str(self.end()) + self._strand + ")"
if __name__ == '__main__':
# loci = [Locus("chr1", 10, 20, "+"),
# Locus("chr1", 18, 22, "+"),
# Locus("chr1", 22, 25, "+"),
# Locus("chr1", 27, 30, "+"),
# Locus("chr1", 28, 31, "+"),
# Locus("chr1", 35, 40, "+"),
# Locus("chr1", 42, 45, "+"),
# Locus("chr1", 43, 44, "+")]
# print unionLoci(loci)
from svviz.variants import Segment, mergedSegments
segments = [Segment("chr100", 1,3, "+", 0),
Segment("chr100", 5, 9, "+", 1),
Segment("chr100", 11, 15, "+", 2),
Segment("chr100", 17, 19, "+", 3),
Segment("chr100", 21, 31, "+", 4),
Segment("chr100", 33, 34, "+", 5)]
print segments
print mergedSegments(segments)